Vietoris-Rips Persistence on Running

Gait-Based Features
Evan Carter, Alexander Rubin, Nikhil Pulimood
Duke University

August 11, 2019

Abstract

This project looks to explore the use of Topological Data Analysis (TDA) in running gait analysis. The major
motivation of this project was to identify biological features that affect a person’s running gait, similar to
how certain features have affected a person’s walking gait. In the process of cleaning our data, we developed
an algorithm to produce the median length of a runner’s stride. After calculating the median stride length,
we performed a persistent homology analysis using a Vietoris-Rips (VR) Complex on this normalized stride
path. Our final results showed that height and speed are directly correlated with the persistent homology of
specific sensors on a runner’s body.

I. Introduction lected the data, placed various sensors across

each runner’s body, as seen in figure 1 be-
unning gait analysis has received a lot

R
low. The runners were then each placed on
of contemporary interest in the field of a treadmill, warmed up, and asked to run at a
gait pattern recognition. Since walking slow pace (2.5 m/s), a medium pace (3.5 m/s),
gait pattern has proven to be a unique human and a fast pace (4.5 m/s). We call these dif-
identifier [1, 2], it was natural for us to try ferent speeds 25, 35, and 45 respectively. The
to understand whether this attribute exists in room with the treadmill was surrounded by
running gait data. Running gait is inherently a motion capturing cameras that collected the
cyclic motion, and thus time series persistent sensor data.
homology made sense as a form of analysis.
An interesting point raised by Lamar-Leon
et al. [3, 2, 4] is that with persistent homol-
ogy, connected components, holes, and cycles
are useful indicators, even as the shape of the
data gets overwhelmed with a large number
of data points. Therefore, with the large num-
ber of data points gathered with running gait
data, persistent homology is a useful tool to
analyze this data in an effective way. Therefore,
we chose to use persistent homology as our
primary tool in analyzing running gait. Figure 1: The Thigh Top Medial sensor is circled green
and the Heel Bottom sensor is circled red.
II. Dataset

i. Set Up ii. Sensors Used

Our data was collected and compiled into an Originally, we planned on looking at all the
open dataset by [5]. The researchers, who col- sensors of the lower leg, since many of the

1
 Persistence on Running Gait • May 2018

papers that we read on gait pattern used this

part of the leg in their analyses. However, we
found that many of our chosen sensors were
difficult to process in MATLAB due to data
corruption. This is why we decided to only
use the thigh top medial and heel bottom on a
runner’s leg. These feature can be seen below
in figure 1.

III. Methods
Below are the steps that we used to normalize
the dataset and perform persistence using a
Figure 2: 450 data points of a runner’s point cloud with
VR-complex:
left foot, 2.5 m/s, and feature thigh top medial.
• Returned the point cloud of a person at an
inputed foot, speed, and feature.
• Ran a sliding window on the point cloud.
that is a very similar to a forward moving
• Returned the critical points of the x-
average with a specified step size. We first
coordinates from the sliding window aver-
initialized an array to hold the averages and
ages.
subsequently iterated through the point cloud
• Removed "fake" critical points (see page 3
with a counter i. During each iteration, we
for more information).
calculated the x,y,z averages of the i row, i + 1
• Returned the median stride path of the
row, i + 2 row, up to i + stepsize row. The
sliding window averages.
sliding window algorithm can be found on
• Returned the max filtration value by calcu-
our GitLab at
lating the max distance between consecu-
https://gitlab.oit.duke.edu/acr43/
tive data points and multiplying by some
running-gait/blob/master/get_sliding_
factor.
window.m.

Point Cloud
After trial-and-error, we developed the above
methods to normalize the dataset in order to
run TDA. Firstly, we calculated a point cloud
by initializing a struct data structure in MAT-
LAB that reads a file for an inputed person and
speed. While iterating through the rows of the
struct, we retrieved the x and y-coordinates of
the inputed feature from each row, and stored
these points in an array. We then exported and
visualized the array. In order to better visualize
the stride paths of the runner, we shrunk the
point cloud by an inputed factor.
Figure 3: 450 data points of a runner’s point cloud with
left foot, 2.5 m/s, and feature thigh top medial
Sliding Window after performing the sliding window with step
In order to clean up the stride paths, we size 20.
implemented a sliding window algorithm

2
 Persistence on Running Gait • May 2018

Critical Points are very important, since when running a

VR-complex on points with uniform gaps,
In the figure above, many of the stride paths
these points in the stride would become
overlap. Consequently, when running a VR-
connected nearly at the same time. We began
complex on the sliding window averages, the
to analyze the local x-maxima, and we realized
complex would detect many unwanted cycles.
that at low speeds, there were several x-values
Therefore, we came up with an approach to
that should not have been considered be local
take the average of all the strides of a runner
maxima. These incorrect values were very
at a particular foot, speed, and feature. In
close to the real local maxima, and thus the
order to do this, we needed to calculate the
calculated time distances between the real
average time of a stride. We assumed that
maxima and the "fake" maxima would be very
the x-coordinates of the runner would be cycli-
minuscule relative to other time distances. This
cal, since the runner would always begin a
would greatly affect our calculated average
new stride after his previous had concluded.
time distance, and would sometimes affect
We considered the time distances between the
the median time distance if there were many
peaks of each stride, and we assumed that each
"fake" local maxima. These "fake" maxima
peak would correspond with a local maximum
points existed primarily at low speeds. We
from the x-coordinates. Therefore, we calcu-
believe that runners are not going to have
lated the time distances between each local
uniform strides at low speeds. We developed
maximum and returned the average of these
an algorithm to remove these points, and the
distances.
code can be found at
https://gitlab.oit.duke.edu/acr43/
Median Stride Path running-gait/blob/master/get_peaks.m.
In order to calculate the average stride of a
runner, we initialized an array with a size
equal to the average time distance. This array
would hold the points of the average stride.
We initiated a counter i that starts at 1 and
ends at the average time distance, and we
iterated through our new initialized array with
this counter. We assigned each row of our
array equal to the average of the point cloud’s
ith row, i + average time distance row, i +2∗
average time distance row, onward. The code
can be found at
https://gitlab.oit.duke.edu/acr43/
running-gait/blob/master/get_median_ Figure 4: "Fake" local maxima from x-coordinates of a
stride_path.m. runner with left foot, 2.5 m/s, and feature
thigh top medial.

"Fake" Critical Points

This did not prove to be effective, as many of
the stride paths were not complete. Instead of
taking the average time distance, we decided
to take the median time distance. This seemed
to work for many of the runners at high
speeds, but at low speeds, we were not getting
uniform gaps between points. Uniform gaps
After removing the "fake" local maxima,
there were still some strides at low speeds that
were not getting completed. We decided to
run our median stride path algorithm on the
averages from our sliding window instead of
on the point cloud. This proved to be highly
effective, and the strides for each runner in
the dataset were completed at any speed. We

3
 Persistence on Running Gait • May 2018
stuck to the median stride instead of the aver-
age stride, since we were unsure if there were
still some "fake" critical points that we were
not detecting with our algorithm.
Figure 5: Median stride of a runner at 2.5 m/s and fea-
ture thigh top medial, using a step size of 20
for the sliding window averages.
Max Filtration Value
After finally calculating the median stride
path, we calculated the max filtration value in
order to run persistence. The algorithm which
we used to calculate the max filtration value
can be found at
https://gitlab.oit.duke.edu/acr43/
running-gait/blob/master/get_distance.
m.
With the median stride path and max filtra-
tion value, we ran a Vietoris-Rips complex on
a Euclidean Metric Space of the median stride
path. We used the Javaplex library in MATLAB
to perform the persistence.
IV. Results
We computed the barcodes of different runners
from the dataset, and we specifically chose
three of these runners for our discussion here.
We chose a runner who was tall, a runner who
had an average height, and a runner who was
short. We analyzed the bar code diagrams of
their thigh top medial and heel bottom at a
slow speed and at a fast speed, 2.5 m/s and 4.5
4
m/s respectively. The shortest runner (Person
13) has a height of 165.2 cm, roughly 5’5". The
average height runner (Person 22) has a height
of 175 cm, roughly 5’9". The tallest runner
(Person 14) has a height of 187.2 cm, roughly
6’1.6".
There are two major take aways from our
TDA analysis. Firstly, the barcodes of the heel
bottom could give a good indication of speed.
At 2.5 m/s, the one dimensional chain of the
heel bottom for both runners terminated be-
tween 255 and 260. At 4.5 m/s, however, the
one-dimensional cycle for both runners termi-
nated between 410 and 420. Secondly, the bar-
codes of the thigh top medial could give a good
indication of height. As seen in figures for the
thigh top medial at a speed of 25, there are two
distinct one dimensional cycles. For Person 14
(tallest), the longest living cycle terminated at
at step 27, whereas Person 13 (shortest) termi-
nated at 16. For person 22 (medium height) the
longest living one dimensional cycle was at 23.
As expected person 23’s termination between
the short and tall person, but interestingly it is
4 steps off from the tall person, and 7 steps off
from the short person. Even though the middle
height is 12.2 cm shorter than the tall, and 9.8
cm taller than the short person. Showing that
the results are not linear because the middle
height termination step is about twice as far
from the short person as the tall.
The persistent homology bar code diagrams
for feature heel-bottom for the three runners
can be found at
https://gitlab.oit.duke.edu/
acr43/running-gait/tree/master/
persistent-homology-diagrams/
heel-bottom.
The persistent homology bar code diagrams
for feature thigh top medial for the three
runners can be found at
https://gitlab.oit.duke.edu/
acr43/running-gait/tree/master/
persistent-homology-diagrams/
thigh-top-medial.
 Persistence on Running Gait • May 2018
Figure 6: Persistent homology of thigh top medial for a
runner with height 165.2 cm and speed 2.5
m/s.
V. Discussion
i. Over Fitting
The nature of our dataset made it necessary
to normalize our data to perform any sort of
analysis. As shown earlier, it was not possible
to perform persistent homology on the original
point cloud because there was close to no rec-
ognizable shape. Our normalization method
created a median stride path, which could be
compared between subjects. The result of this
method can be seen in figure 8. We found dif-
ferences in the subjects’ stride paths and drew
conclusions with this data. (show image)
Unfortunately, it is possible that our
normalization techniques could cause us to
lose some aspects of a runner’s gait pattern.
Perturbations that can be seen in our removal
of "fake" local maxima may be important
features that we are smoothing. We developed
a time series animation of a runner’s strides
along with his median stride path in order to
visualize any stride details that we could be
losing with our normalization techniques. The
video can be found at
https://gitlab.oit.duke.edu/acr43/
running-gait/blob/master/Thigh_Heel_
Path_Animation%20(Converted).mov.
While the sliding window was originally im-
portant to clear up the data for our stride path
Figure 7: Persistent homology of thigh top medial for a
runner with height 187.2 cm and speed 2.5
m/s.
Figure 8: Point cloud of thigh top medial, which was
normalized using the sliding window algo-
rithm with step size 20 and then the median
stride path algorithm.
algorithm, we later found that modifications to
the algorithm make the sliding window unnec-
essary. If we were to continue our research, we
would remove the effect of the sliding window
and hopefully retain some lost information.
Since a gait pattern is considered to be similar
to a fingerprint, these fine details may be es-
sential components for our analysis. Moreover,
the main form of our analysis uses TDA, and
thus the general shape of the data is the most
important aspect. While the exact shape of the
stride can change, the number of connected
components and the overall homology of the
data stays consistent [2].
5
 Persistence on Running Gait • May 2018
ii. Further Research
There are some areas of research which would
have been interesting directions to explore,
which we either did not have the data for or
resources to pursue. When there are better
data science tools, there will be better meth-
ods for helping treatment with injury and and
biomechanical research. [6]
Injury
The effects of injury on running gait would
have been an interesting area to analyze us-
ing persistent homology. In a prior study, re-
searchers were able to discern differences in the
kinematic gait patterns of healthy and patho-
logical runners [7]. These differences occurred
in the frontal and sagittal plane knee angles
(P<0.001), independent of age, height, weight,
and running speed. The dataset we used does
have some injury data, but in order to under-
stand that effect of injury, we would need data
from the subjects before and after injury which
is not available. If we could find more features
(such as height, weight, etc.) that can be used
to classify the persistent homology of subjects’
gait patterns then we could compare subjects
with similar features and then observe the ef-
fects of injury between these subjects.
Biological Sex Classification
When we started this project, we began our
research by reading Lamar-Leon et al [3, 2]
who used gait pattern to classify a runner’s
biological sex. Like other papers on gait recog-
nition that used persistent homology, this pa-
per used computer vision technology to gather
data about the subject’s gait. Interested by this
classification technique, we planned to explore
whether these findings in walking gait pattern
translated to running gait. Unfortunately, the
dataset we used only provided data for one
female subject, making it difficult to do any
sort of classification.
6
Running Form
One area that would have also been interest-
ing to explore would have been an analysis
of running form efficiency and its relationship
to persistent homology. A runner’s form is
not readily available, since we do not have the
videos of our runners. However, we could po-
tentially recreate the motion using an animated
point cloud with all the features. We started
to visualize this in the animation link above.
Given our experience with this type of anima-
tion and the subjective nature of classifying
running form efficiency, analyzing this data
could prove challenging.
The dataset does include the foot-strike pat-
tern of each subject. Mid-foot and fore-foot
strike patterns are considered to be more effi-
cient than heel-strikes, so it would be interest-
ing to explore whether the foot-strike pattern
affects the persistent homology of a running
gait. It is also possible that other researchers
have performed running form efficiency anal-
ysis on this specific open dataset, and those
results would be helpful if we decided to do
this type of analysis.
Competitive vs. Elite
In a similar vein as running form, the competi-
tion level of a runner would be an interesting
variable to explore with persistent homology.
The dataset classifies a subjects’ competition
levels using the designations "Competitive"
and "Elite," but we are unable to determine
how this classification is made. The dataset
does provide a runner’s preferred race distance
and their pace at this distance. It would be in-
teresting for us to independently compare a
subject’s ability to the abilities of other com-
petitive runners, and thus make our own com-
petitive classification. We could use this to
compare our gait analysis.
 Persistence on Running Gait • May 2018

References
[1] A. Phinyomark, G. Petri, E. Ibáñez-Marcelo, S. T. Osis, and R. Ferber, “Analysis of big data
in gait biomechanics: Current trends and future directions,” Journal of Medical and Biological
Engineering, Jul 2017.

[2] J. Lamar-Leon, R. A. Baryolo, E. Garcia-Reyes, and R. Gonzalez-Diaz, “Gait-based carried

object detection using persistent homology,” in Progress in Pattern Recognition, Image Analysis,
Computer Vision, and Applications (E. Bayro-Corrochano and E. Hancock, eds.), (Cham), pp. 836–
843, Springer International Publishing, 2014.

[3] J. Lamar-León, R. A. Baryolo, E. B. G. Reyes, and R. González-Díaz, “Persistent-homology-

based gait recognition,” CoRR, vol. abs/1707.06982, 2017.

[4] J. L. Leon, A. Cerri, E. G. Reyes, and R. G. Diaz, “Gait-based gender classification using
persistent homology,” in Progress in Pattern Recognition, Image Analysis, Computer Vision, and
Applications (J. Ruiz-Shulcloper and G. Sanniti di Baja, eds.), (Berlin, Heidelberg), pp. 366–373,
Springer Berlin Heidelberg, 2013.

[5] R. Fukuchi, C. A. Fukuchi, and M. Duarte, “A public data set of running biomechanics and
the effects of running speed on lower extremity kinematics and kinetics,” 3 2017.

[6] R. Ferber, S. Osis, J. Hicks, and S. Delp, “Gait biomechanics in the era of data science,” Journal
of Biomechanics, vol. 49, 10 2016.

[7] A. Phinyomark, S. Osis, B. Hettinga, and R. Ferber, “Kinematic gait patterns in healthy runners:
A hierarchical cluster analysis,” Journal of Biomechanics, vol. 48, p. 3897–3904, 11 2015.