stepPattern: Step patterns for DTW
In dtw: Dynamic Time Warping Algorithms
stepPattern R Documentation
Step patterns for DTW
Description
A stepPattern object lists the transitions allowed while searching
for the minimum-distance path. DTW variants are implemented by passing one
of the objects described in this page to the stepPattern argument of
the dtw() call.
Usage
## S3 method for class 'stepPattern'
t(x)
## S3 method for class 'stepPattern'
plot(x, ...)
## S3 method for class 'stepPattern'
print(x, ...)
rabinerJuangStepPattern(type, slope.weighting = "d", smoothed = FALSE)
Arguments
x
a step pattern object
...
additional arguments to print().
type
path specification, integer 1..7 (see (Rabiner1993), table 4.5)
slope.weighting
slope weighting rule: character "a" to "d" (see (Rabiner1993), sec. 4.7.2.5)
smoothed
logical, whether to use smoothing (see (Rabiner1993), fig. 4.44)
Details
A step pattern characterizes the matching model and slope constraint
specific of a DTW variant. They also known as local- or slope-constraints,
transition types, production or recursion rules (GiorginoJSS).
Pre-defined step patterns
## Well-known step patterns
symmetric1
symmetric2
asymmetric
## Step patterns classified according to Rabiner-Juang (Rabiner1993)
rabinerJuangStepPattern(type,slope.weighting="d",smoothed=FALSE)
## Slope-constrained step patterns from Sakoe-Chiba (Sakoe1978)
symmetricP0; asymmetricP0
symmetricP05; asymmetricP05
symmetricP1; asymmetricP1
symmetricP2; asymmetricP2
## Step patterns classified according to Rabiner-Myers (Myers1980)
typeIa; typeIb; typeIc; typeId;
typeIas; typeIbs; typeIcs; typeIds; # smoothed
typeIIa; typeIIb; typeIIc; typeIId;
typeIIIc; typeIVc;
## Miscellaneous
mori2006;
rigid;
A variety of classification schemes have been proposed for step patterns, including
Sakoe-Chiba (Sakoe1978); Rabiner-Juang (Rabiner1993); and Rabiner-Myers
(Myers1980). The dtw package implements all of the transition types
found in those papers, with the exception of Itakura's and
Velichko-Zagoruyko's steps, which require subtly different algorithms (this
may be rectified in the future). Itakura recursion is almost, but not quite,
equivalent to typeIIIc.
For convenience, we shall review pre-defined step patterns grouped by
classification. Note that the same pattern may be listed under different
names. Refer to paper (GiorginoJSS) for full details.
1. Well-known step patterns
Common DTW implementations are based on one of the following transition
types.
symmetric2 is the normalizable, symmetric, with no local slope
constraints. Since one diagonal step costs as much as the two equivalent
steps along the sides, it can be normalized dividing by N+M
(query+reference lengths). It is widely used and the default.
asymmetric is asymmetric, slope constrained between 0 and 2. Matches
each element of the query time series exactly once, so the warping path
index2~index1 is guaranteed to be single-valued. Normalized by
N (length of query).
symmetric1 (or White-Neely) is quasi-symmetric, no local constraint,
non-normalizable. It is biased in favor of oblique steps.
2. The Rabiner-Juang set
A comprehensive table of step patterns is proposed in Rabiner-Juang's book
(Rabiner1993), tab. 4.5. All of them can be constructed through the
rabinerJuangStepPattern(type,slope.weighting,smoothed) function.
The classification foresees seven families, labelled with Roman numerals
I-VII; here, they are selected through the integer argument type.
Each family has four slope weighting sub-types, named in sec. 4.7.2.5 as
"Type (a)" to "Type (d)"; they are selected passing a character argument
slope.weighting, as in the table below. Furthermore, each subtype can
be either plain or smoothed (figure 4.44); smoothing is enabled setting the
logical argument smoothed. (Not all combinations of arguments make
sense.)
Subtype | Rule | Norm | Unbiased
--------|------------|------|---------
a | min step | -- | NO
b | max step | -- | NO
c | Di step | N | YES
d | Di+Dj step | N+M | YES
3. The Sakoe-Chiba set
Sakoe-Chiba (Sakoe1978) discuss a family of slope-constrained patterns; they
are implemented as shown in page 47, table I. Here, they are called
symmetricP<x> and asymmetricP<x>, where <x> corresponds
to Sakoe's integer slope parameter P. Values available are
accordingly: 0 (no constraint), 1, 05 (one half) and
2. See (Sakoe1978) for details.
4. The Rabiner-Myers set
The type<XX><y> step patterns follow the older Rabiner-Myers'
classification proposed in (Myers1980) and (MRR1980). Note that this is a
subset of the Rabiner-Juang set (Rabiner1993), and the latter should be
preferred in order to avoid confusion. <XX> is a Roman numeral
specifying the shape of the transitions; <y> is a letter in the range
a-d specifying the weighting used per step, as above; typeIIx
patterns also have a version ending in s, meaning the smoothing is
used (which does not permit skipping points). The typeId, typeIId and
typeIIds are unbiased and symmetric.
5. Others
The rigid pattern enforces a fixed unitary slope. It only makes sense
in combination with open.begin=TRUE, open.end=TRUE to find gapless
subsequences. It may be seen as the P->inf limiting case in Sakoe's classification.
mori2006 is Mori's asymmetric step-constrained pattern (Mori2006). It
is normalized by the matched reference length.
mvmStepPattern() implements Latecki's Minimum Variance
Matching algorithm, and it is described in its own page.
Methods
print.stepPattern prints an user-readable description of the
recurrence equation defined by the given pattern.
plot.stepPattern graphically displays the step patterns productions
which can lead to element (0,0). Weights are shown along the step leading to
the corresponding element.
t.stepPattern transposes the productions and normalization hint so
that roles of query and reference become reversed.
Note
Constructing stepPattern objects is tricky and thus undocumented. For a commented example please see source code for symmetricP1.
Author(s)
Toni Giorgino
References
(GiorginoJSS) Toni Giorgino. Computing and Visualizing
Dynamic Time Warping Alignments in R: The dtw Package. Journal of
Statistical Software, 31(7), 1-24. doi: 10.18637/jss.v031.i07
(Itakura1975) Itakura, F., Minimum prediction residual
principle applied to speech recognition, Acoustics, Speech, and Signal
Processing, IEEE Transactions on , vol.23, no.1, pp. 67-72, Feb 1975.
doi: 10.1109/TASSP.1975.1162641
(MRR1980) Myers,
C.; Rabiner, L. & Rosenberg, A. Performance tradeoffs in dynamic time
warping algorithms for isolated word recognition, IEEE Trans. Acoust.,
Speech, Signal Process., 1980, 28, 623-635.
doi: 10.1109/TASSP.1980.1163491
(Mori2006) Mori,
A.; Uchida, S.; Kurazume, R.; Taniguchi, R.; Hasegawa, T. & Sakoe, H. Early
Recognition and Prediction of Gestures Proc. 18th International Conference
on Pattern Recognition ICPR 2006, 2006, 3, 560-563.
doi: 10.1109/ICPR.2006.467
(Myers1980) Myers,
Cory S. A Comparative Study Of Several Dynamic Time Warping
Algorithms For Speech Recognition, MS and BS thesis, Dept. of Electrical
Engineering and Computer Science, Massachusetts Institute of Technology,
archived Jun 20 1980, https://hdl.handle.net/1721.1/27909
(Rabiner1993) Rabiner, L. R., & Juang, B.-H. (1993). Fundamentals of
speech recognition. Englewood Cliffs, NJ: Prentice Hall.
(Sakoe1978) Sakoe, H.; Chiba, S., Dynamic programming algorithm
optimization for spoken word recognition, Acoustics, Speech, and Signal
Processing, IEEE Transactions on , vol.26, no.1, pp. 43-49, Feb 1978
doi: 10.1109/TASSP.1978.1163055
See Also
mvmStepPattern(), implementing Latecki's Minimal
Variance Matching algorithm.
Examples
#########
##
## The usual (normalizable) symmetric step pattern
## Step pattern recursion, defined as:
## g[i,j] = min(
## g[i,j-1] + d[i,j] ,
## g[i-1,j-1] + 2 * d[i,j] ,
## g[i-1,j] + d[i,j] ,
## )
print(symmetric2) # or just "symmetric2"
#########
##
## The well-known plotting style for step patterns
plot(symmetricP2,main="Sakoe's Symmetric P=2 recursion")
#########
##
## Same example seen in ?dtw , now with asymmetric step pattern
idx<-seq(0,6.28,len=100);
query<-sin(idx)+runif(100)/10;
reference<-cos(idx);
## Do the computation
asy<-dtw(query,reference,keep=TRUE,step=asymmetric);
dtwPlot(asy,type="density",main="Sine and cosine, asymmetric step")
#########
##
## Hand-checkable example given in [Myers1980] p 61
##
`tm` <-
structure(c(1, 3, 4, 4, 5, 2, 2, 3, 3, 4, 3, 1, 1, 1, 3, 4, 2,
3, 3, 2, 5, 3, 4, 4, 1), .Dim = c(5L, 5L))
dtw documentation built on Sept. 20, 2022, 1:06 a.m.
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| stepPattern | R Documentation |
Step patterns for DTW
Description
A stepPattern object lists the transitions allowed while searching
for the minimum-distance path. DTW variants are implemented by passing one
of the objects described in this page to the stepPattern argument of
the dtw() call.
Usage
## S3 method for class 'stepPattern' t(x) ## S3 method for class 'stepPattern' plot(x, ...) ## S3 method for class 'stepPattern' print(x, ...) rabinerJuangStepPattern(type, slope.weighting = "d", smoothed = FALSE)
Arguments
x |
a step pattern object |
... |
additional arguments to |
type |
path specification, integer 1..7 (see (Rabiner1993), table 4.5) |
slope.weighting |
slope weighting rule: character |
smoothed |
logical, whether to use smoothing (see (Rabiner1993), fig. 4.44) |
Details
A step pattern characterizes the matching model and slope constraint specific of a DTW variant. They also known as local- or slope-constraints, transition types, production or recursion rules (GiorginoJSS).
Pre-defined step patterns
## Well-known step patterns symmetric1 symmetric2 asymmetric ## Step patterns classified according to Rabiner-Juang (Rabiner1993) rabinerJuangStepPattern(type,slope.weighting="d",smoothed=FALSE) ## Slope-constrained step patterns from Sakoe-Chiba (Sakoe1978) symmetricP0; asymmetricP0 symmetricP05; asymmetricP05 symmetricP1; asymmetricP1 symmetricP2; asymmetricP2 ## Step patterns classified according to Rabiner-Myers (Myers1980) typeIa; typeIb; typeIc; typeId; typeIas; typeIbs; typeIcs; typeIds; # smoothed typeIIa; typeIIb; typeIIc; typeIId; typeIIIc; typeIVc; ## Miscellaneous mori2006; rigid;
A variety of classification schemes have been proposed for step patterns, including
Sakoe-Chiba (Sakoe1978); Rabiner-Juang (Rabiner1993); and Rabiner-Myers
(Myers1980). The dtw package implements all of the transition types
found in those papers, with the exception of Itakura's and
Velichko-Zagoruyko's steps, which require subtly different algorithms (this
may be rectified in the future). Itakura recursion is almost, but not quite,
equivalent to typeIIIc.
For convenience, we shall review pre-defined step patterns grouped by classification. Note that the same pattern may be listed under different names. Refer to paper (GiorginoJSS) for full details.
1. Well-known step patterns
Common DTW implementations are based on one of the following transition types.
symmetric2 is the normalizable, symmetric, with no local slope
constraints. Since one diagonal step costs as much as the two equivalent
steps along the sides, it can be normalized dividing by N+M
(query+reference lengths). It is widely used and the default.
asymmetric is asymmetric, slope constrained between 0 and 2. Matches
each element of the query time series exactly once, so the warping path
index2~index1 is guaranteed to be single-valued. Normalized by
N (length of query).
symmetric1 (or White-Neely) is quasi-symmetric, no local constraint,
non-normalizable. It is biased in favor of oblique steps.
2. The Rabiner-Juang set
A comprehensive table of step patterns is proposed in Rabiner-Juang's book
(Rabiner1993), tab. 4.5. All of them can be constructed through the
rabinerJuangStepPattern(type,slope.weighting,smoothed) function.
The classification foresees seven families, labelled with Roman numerals
I-VII; here, they are selected through the integer argument type.
Each family has four slope weighting sub-types, named in sec. 4.7.2.5 as
"Type (a)" to "Type (d)"; they are selected passing a character argument
slope.weighting, as in the table below. Furthermore, each subtype can
be either plain or smoothed (figure 4.44); smoothing is enabled setting the
logical argument smoothed. (Not all combinations of arguments make
sense.)
Subtype | Rule | Norm | Unbiased
--------|------------|------|---------
a | min step | -- | NO
b | max step | -- | NO
c | Di step | N | YES
d | Di+Dj step | N+M | YES
3. The Sakoe-Chiba set
Sakoe-Chiba (Sakoe1978) discuss a family of slope-constrained patterns; they
are implemented as shown in page 47, table I. Here, they are called
symmetricP<x> and asymmetricP<x>, where <x> corresponds
to Sakoe's integer slope parameter P. Values available are
accordingly: 0 (no constraint), 1, 05 (one half) and
2. See (Sakoe1978) for details.
4. The Rabiner-Myers set
The type<XX><y> step patterns follow the older Rabiner-Myers'
classification proposed in (Myers1980) and (MRR1980). Note that this is a
subset of the Rabiner-Juang set (Rabiner1993), and the latter should be
preferred in order to avoid confusion. <XX> is a Roman numeral
specifying the shape of the transitions; <y> is a letter in the range
a-d specifying the weighting used per step, as above; typeIIx
patterns also have a version ending in s, meaning the smoothing is
used (which does not permit skipping points). The typeId, typeIId and
typeIIds are unbiased and symmetric.
5. Others
The rigid pattern enforces a fixed unitary slope. It only makes sense
in combination with open.begin=TRUE, open.end=TRUE to find gapless
subsequences. It may be seen as the P->inf limiting case in Sakoe's classification.
mori2006 is Mori's asymmetric step-constrained pattern (Mori2006). It
is normalized by the matched reference length.
mvmStepPattern() implements Latecki's Minimum Variance
Matching algorithm, and it is described in its own page.
Methods
print.stepPattern prints an user-readable description of the
recurrence equation defined by the given pattern.
plot.stepPattern graphically displays the step patterns productions
which can lead to element (0,0). Weights are shown along the step leading to
the corresponding element.
t.stepPattern transposes the productions and normalization hint so
that roles of query and reference become reversed.
Note
Constructing stepPattern objects is tricky and thus undocumented. For a commented example please see source code for symmetricP1.
Author(s)
Toni Giorgino
References
(GiorginoJSS) Toni Giorgino. Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package. Journal of Statistical Software, 31(7), 1-24. doi: 10.18637/jss.v031.i07
(Itakura1975) Itakura, F., Minimum prediction residual principle applied to speech recognition, Acoustics, Speech, and Signal Processing, IEEE Transactions on , vol.23, no.1, pp. 67-72, Feb 1975. doi: 10.1109/TASSP.1975.1162641
(MRR1980) Myers, C.; Rabiner, L. & Rosenberg, A. Performance tradeoffs in dynamic time warping algorithms for isolated word recognition, IEEE Trans. Acoust., Speech, Signal Process., 1980, 28, 623-635. doi: 10.1109/TASSP.1980.1163491
(Mori2006) Mori, A.; Uchida, S.; Kurazume, R.; Taniguchi, R.; Hasegawa, T. & Sakoe, H. Early Recognition and Prediction of Gestures Proc. 18th International Conference on Pattern Recognition ICPR 2006, 2006, 3, 560-563. doi: 10.1109/ICPR.2006.467
(Myers1980) Myers, Cory S. A Comparative Study Of Several Dynamic Time Warping Algorithms For Speech Recognition, MS and BS thesis, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, archived Jun 20 1980, https://hdl.handle.net/1721.1/27909
(Rabiner1993) Rabiner, L. R., & Juang, B.-H. (1993). Fundamentals of speech recognition. Englewood Cliffs, NJ: Prentice Hall.
(Sakoe1978) Sakoe, H.; Chiba, S., Dynamic programming algorithm optimization for spoken word recognition, Acoustics, Speech, and Signal Processing, IEEE Transactions on , vol.26, no.1, pp. 43-49, Feb 1978 doi: 10.1109/TASSP.1978.1163055
See Also
mvmStepPattern(), implementing Latecki's Minimal
Variance Matching algorithm.
Examples
######### ## ## The usual (normalizable) symmetric step pattern ## Step pattern recursion, defined as: ## g[i,j] = min( ## g[i,j-1] + d[i,j] , ## g[i-1,j-1] + 2 * d[i,j] , ## g[i-1,j] + d[i,j] , ## ) print(symmetric2) # or just "symmetric2" ######### ## ## The well-known plotting style for step patterns plot(symmetricP2,main="Sakoe's Symmetric P=2 recursion") ######### ## ## Same example seen in ?dtw , now with asymmetric step pattern idx<-seq(0,6.28,len=100); query<-sin(idx)+runif(100)/10; reference<-cos(idx); ## Do the computation asy<-dtw(query,reference,keep=TRUE,step=asymmetric); dtwPlot(asy,type="density",main="Sine and cosine, asymmetric step") ######### ## ## Hand-checkable example given in [Myers1980] p 61 ## `tm` <- structure(c(1, 3, 4, 4, 5, 2, 2, 3, 3, 4, 3, 1, 1, 1, 3, 4, 2, 3, 3, 2, 5, 3, 4, 4, 1), .Dim = c(5L, 5L))
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