Cough Characterizations A Fractal Characterization of Cough Signals

2021-07-29 For Covid-19 Pre-Screening Applications

Y. Bandung1 M.W. Langi2 K. Mutijarsa1 A.Z.R. Langi1

International Conference on ICT for Smart Society, 2021
1 InformationTechnology RG,
School of Electrical Engineering and Informatics, ITB Indonesia

2 PhysicsStudy Program
Faculty of Mathematics and Natural Sciences, ITB Indonesia

Thank you Chairman/Chairwoman and good morning ladies and gentlemen and thank you for
giving me the opportunity to present our paper. My name is xxxx, I am a (student/professor)
at xxxx, and I will present This paper on behalf of us the authors with a title “ A Fractal
Characterization of Cough Signals.
 Cough Characterizations
Outline

2021-07-29 Coughs Processing In Non Intrusive

Prescreening
Correlation Fractal Dimension of Signals
An Application to Coughs
Concluding Remarks

Outline

1. This paper report a correlation fractal dimension characterization as applied to auditory

cough signals. We have obtained cough samples from persons with and without Covid-19
disease. Our hypothesis is coughs coming from Covid-19 disease exhibit fractal behavior.
To show this, we apply fractal-size measurements on both samples. Preliminary results
confirm fractality on Covid-19 cough signals. This result can improve performance of
pre-screening for identification the presence respiratory diseases, such as Covid-19.
2. The outline of my talk is as follow. First I mention the importance of valid and
meaningful characterization of coughs in prescreening applications
3. After that I explain Correlation dimension and how is is applied to signal measurements
4. Next I will explain how We have used this approach to characterize Coughs coming from
Virufy database
5. Finally I will conclude with remarks
 Cough Characterizations
Nonintrusive Prescreening Through Coughs

Likely, Not

2021-07-29
Machine

Coughs Processing In Non Intrusive Prescreening

Coughs Recording Processing Modeling Likely, Un-
Learning
certain

1. Coughs waveform of a suspect are recorded.

2. Signal processing system characterizes the coughs waveform
3. Modeling extracts parameters according to a model

Nonintrusive Prescreening Through Coughs

4. Machine learning and classifiers determine whether it is likely, unlikely, or
uncertain a suspect has a respiratory disease.

1. A prescreening system is as follows.

2. Coughs waveform of a suspect are recorded.
3. Signal processing system characterizes the coughs waveform
4. Modeling extracts parameters according to a model
5. Machine learning and classifiers determine whether it is likely, unlikely, or uncertain a
suspect has a respiratory disease.
6. Clearely Nonintrusive Prescreening Depends on Signal Characterizations
7. Any Characterizations Must be based on Valid and Meaningful measurements
 Cough Characterizations
A Measurement System

Singularity-
Singularity
Strength Strength

2021-07-29
Estimation

Correlation Fractal Dimension of Signals Measure

Signal Counting Size Calculation Size
Mapping

(1) Construct Vectors of m−Dimension of scale r .

(2) Count Correlation Sum C (m, rk ) for scale rk .

A Measurement System (3) Use linear regression log C (m, rk ) = log S + D log rk−1 to estimate critical exponent
D and residue C .
(4) Calculate Size S ≈ Sk = C (rk ) rk−D

1. To study fractality of cougs, we apply the fractal-size measurements on both samples.

The measurement system works as follows
2. In step 1 Construct Vectors of M-Dimension of scale r. Here M must be larger than D.
However since we do not know D yet, we try several M=1,2,..., 10
3. In step 2 Count Correlation Sum C (M, rk ) for scale r_k
4. in step 4 Estimate critical exponent D and residue C using linear regression on log-log plot
5. Finaly in step 5 Calculate Size
 Cough Characterizations
Calibration Using Henon Signal

2021-07-29 Correlation Fractal Dimension of Signals

Henon
1.5 1.5
'henon5000.data'

1 1

0.5
0.5

Amplitude
0

y
0
-0.5

-0.5
-1

-1
-1.5
-1.5 -1 -0.5 0 0.5 1 1.5

Calibration Using Henon Signal

-1.5 x

0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.1
Time [s]

1. But before that, We use Henon signal to calibratae the Size Measurement of Signal since
its dimension is known
 Cough Characterizations
Calibration Results

2021-07-29
henon.r5000.dat, N=, Delay=1, Theiler Windows=50, Gaussian kernel Henon Signal Sizes

Correlation Fractal Dimension of Signals

3
Estimates Estimates
1.2

2.5
1

Correlation Dimension
0.8

Signal Size
1.5
0.6

1
0.4

0.5 0.2

Calibration Results
0 0
0.01 0.1 1 0.01 0.1 1

Disk Radius Disc Diameters

1. The measurement resul;t in two graphs. The first one is dimension estimation, and the
second one the size at tyhat dimension.
2. Recall we construct vectors m dimensional, from m=1 to 10. as a result there are 10
curves corresponding to 10 measurement dimensions.
3. From this calibration we know to look at disk scale between 0.01 and 0.1. THe valid
signal size is the second line from above
 Cough Characterizations Sample #
083
Covid
N
Voice
Cough
Sex
M
Age
53
Coughs
18

2021-07-29
084 P Cough M 50 8

An Application to Coughs
085 N Cough M 43 2
086 P Cough M 65 9
Virufy Coughs
087 P Cough F 40 7
Database: Cough
088 N Cough F 66 7
segments from16
089 N Cough F 20 5
patients, 7
positive 090 N Cough F 17 8
COVID-19, Total 091 N Cough M 47 8
106 Segments 092 P Cough M 53 9
093 P Cough F 24 5
094 P Cough M 51 7
095 N Cough M 53 16
096 P Cough M 32 4
097 N Cough M 37 5
098 N Cough F 24 3

1. We have obtained cough samples from person with and without Covid-19 disease (Virufy
Database). Cough segments from16 patients, 7 positive COVID-19, Total 106 Segments
 Cough Characterizations
While Visually Similar, Cough Segments Exhibit Different Singularies

2021-07-29
Case neg-0421-083-cough-m-53 Case pos-0421-084-cough-m-50

An Application to Coughs
0.8
0.6

0.6

0.4
0.4

0.2
0.2

Amplitude

Amplitude
0 0

-0.2
-0.2

-0.4
-0.4

-0.6

-0.6
-0.8
0 0.1 0.2 0.3 0.4 0.5 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5
Time [s] Time [s]

Left: A segment of Sample Right: A segment of Sample

While Visually Similar, Cough Segments Exhibit Different 083 (negative Covid-19). 084 (positive Covid-19).

Singularies
1. On the left Cough Sample 83-17 tested negative COVID-19. On the right Cough Sample
084-8 tested positive. They area very similar visually. Our hypothesis is coughs coming
from Covid-19 disease exhibit fractal behavior.
 Cough Characterizations
Coughs samples from nine patients tested negative COVID-19
Case = neg-0421-085-cough-m-43
0.8
'neg085.dat'

0.6

2021-07-29
0.4

An Application to Coughs
0.2

Signal
0

-0.2

-0.4

-0.6

-0.8
0 5000 10000 15000 20000 25000
Samples

Coughs samples from nine patients tested negative COVID-19

1. These are samples from other patients tested negative of COVID-19

 Cough Characterizations
Coughs samples from nine patients tested negative COVID-19

2021-07-29 An Application to Coughs

Coughs samples from nine patients tested negative COVID-19

1. These are samples from other patients tested negative of COVID-19

 Cough Characterizations
Coughs samples from seven patients tested positive COVID-19
Case=pos-0421-084-cough-m-50 Case=pos-0421-086-cough-m-65 Case=pos-0421-087-cough-f-40
0.8 0.8 0.8
'pos084.dat' 'pos086.dat' 'pos087.dat'

0.6 0.6 0.6

2021-07-29
0.4 0.4 0.4

An Application to Coughs
0.2 0.2 0.2

Signals

Signals

Signals
0 0 0

-0.2 -0.2 -0.2

-0.4 -0.4 -0.4

-0.6 -0.6 -0.6

-0.8 -0.8 -0.8

0 5000 10000 15000 20000 25000 30000 35000 0 5000 10000 15000 20000 25000 30000 0 5000 10000 15000 20000 25000
Samples Samples Samples

Case=pos-0421-092-cough-m-53 Case=pos-0421-093-cough-f-24 Case=pos-0421-094-cough-m-51

0.8 1 0.8
'pos092.dat' 'pos093.dat' 'pos094.dat'

0.6 0.8 0.6

0.6
0.4 0.4

0.4

Coughs samples from seven patients tested positive COVID-19

0.2 0.2

0.2

Signals

Signals

Signals
0 0
0

-0.2 -0.2
-0.2

-0.4 -0.4
-0.4

-0.6 -0.6 -0.6

-0.8 -0.8 -0.8

0 5000 10000 15000 20000 25000 30000 35000 40000 0 5000 10000 15000 20000 25000 30000 0 5000 10000 15000 20000 25000 30000 35000
Samples Samples Samples

1. These are samples from other patients tested positive of COVID-19

 Cough Characterizations
Coughs samples from seven patients tested positive COVID-19

2021-07-29 An Application to Coughs 0.8

0.6
1
Case=pos-0422-096-cough-m-31

'pos096.dat'

0.4

0.2

Signals
0

-0.2

-0.4

-0.6

-0.8

-1
0 5000 10000 15000 20000 25000 30000 35000 40000 45000 50000

Coughs samples from seven patients tested positive COVID-19

Samples

1. These are samples from other patients tested positive of COVID-19.

2. They look very similar
 Cough Characterizations
Fractality of Coughs
File = pos-0421-084-cough-m-50.dat, Delay = 1, Theiler Windows = 50, Gaussian kernel

3
Estimates
File = neg-0421-083-cough-m-53.dat, Delay = 1, Theiler Windows = 50, Gaussian kernel

3 2.5

2021-07-29
Estimates

An Application to Coughs
2.5 2

Correlation Dimension
2 1.5

Correlation Dimension
1.5 1

1 0.5

0.5 0
0.01 0.1 1

Disk Radius
0
0.01 0.1 1

Disk Radius
Right: Dimension estimations
Left: Dimension estimations of of Sample 084 (positive

Fractality of Coughs
Sample 083 (negative Covid-19) converge at
Covid-19) do not converge, 0.01 < r < 0.1, indicating
indicating no fractality. existence of fractality at
D ≈ 0.70.

1. We have performed the above process on the two samples, Sample 083 and 084, resulting
in two different characteristics. Shown in here, results from Sample 083 (patient with
negative Corona disease) does not exhibit fractal behaviour. It shows more noise-like
behaviors with no plateau to identify.
2. In contrast results from Sample 084 (patient with positive Corona-19) exhibit converging
plateau at D = 0.70 on certain range of radii (0.01 < r < 0.1). This concludes that the
cough contains fractals at Dimension 0.70.
3. this Preliminary results suggest fractality on Covid-19 cough signals.
 Cough Characterizations
Signal dimension estimation from nine patients tested negative COVID-19
File = neg-0421-085-cough-m-43.dat, Delay = 1, Theiler Windows = 50, Gaussian kernel
3
'neg085.plot' using 1:3

2021-07-29
2.5

An Application to Coughs
2

Correlation Dimension
1.5

0.5

0
0.01 0.1 1
Disk Radius

File = neg-0421-089-cough-f-20.dat, Delay = 1, Theiler Windows = 50, Gaussian kernel

3
'neg089.plot' using 1:3

2.5

Correlation Dimension
Signal dimension estimation from nine patients tested negative
1.5

0.5

0
0.01 0.1 1

COVID-19
Disk Radius

1. These are dimension estimates on Negative coughs

 Cough Characterizations
Signal dimension estimation from nine patients tested negative COVID-19

2021-07-29 An Application to Coughs

Signal dimension estimation from nine patients tested negative

COVID-19
1. These are dimension estimates on Negative coughs
 Cough Characterizations
Size calculation from nine patients tested negative COVID-19
File = neg-0421-083-cough-m-53.dat, Delay = 1, Theiler Windows = 50 File = neg-0421-085-cough-m-43.dat, Delay = 1, Theiler Windows = 50 File = neg-0421-088-cough-f-66.dat, Delay = 1, Theiler Windows = 50
25 6
'neg083.cr' u 1:4 'neg085.cr' u 1:4 'neg088.cr' u 1:4
14

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5
12 20

An Application to Coughs
10 4

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Sizes

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3

6 10

5
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Disk Radius Disk Radius Disk Radius

File = neg-0421-089-cough-f-20.dat, Delay = 1, Theiler Windows = 50 File = neg-0421-090-cough-f-17.dat, Delay = 1, Theiler Windows = 50 File = neg-0421-091-cough-m-47.dat, Delay = 1, Theiler Windows = 50
8 8
'neg089.cr' u 1:4 'neg090.cr' u 1:4 'neg091.cr' u 1:4
30
7 7

25
6 6

Size calculation from nine patients tested negative COVID-19

5 20 5

Sizes

Sizes

Sizes
4 4
15

3 3
10

2 2

5
1 1

0 0 0
0.01 0.1 1 0.01 0.1 1 0.01 0.1 1
Disk Radius Disk Radius Disk Radius

1. These are corresponding signal sizes estimated on Negative coughs

 Cough Characterizations
Size calculation from nine patients tested negative COVID-19

2021-07-29 An Application to Coughs 90

80
File = neg-0422-095-cough-m-53.dat, Delay = 1, Theiler Windows = 50

'neg095.cr' u 1:4
10

8
File = neg-0422-097-cough-m-37.dat, Delay = 1, Theiler Windows = 50

'neg097.cr' u 1:4
5

4
File = neg-0422-098-cough-f-24.dat, Delay = 1, Theiler Windows = 50

'neg098.cr' u 1:4

70

60
6 3

Sizes
50

Sizes

Sizes
40
4 2

30

20 2 1

10

0 0 0
0.01 0.1 1 0.01 0.1 1 0.01 0.1 1

Size calculation from nine patients tested negative COVID-19

Disk Radius Disk Radius Disk Radius

1. These are corresponding signal sizes estimated on Negative coughs

 Cough Characterizations
Signal dimension estimation from seven patients tested positive COVID-19
File=pos-0421-084-cough-m-50, Delay = 1, Theiler Windows = 50, Gaussian kernel File=pos-0421-086-cough-m-65, Delay = 1, Theiler Windows = 50, Gaussian kernel File=pos-0421-087-cough-f-40, Delay = 1, Theiler Windows = 50, Gaussian kernel
3 3 3
'pos084.plot' using 1:3 'pos086.plot' using 1:3 'pos087.plot' using 1:3

2021-07-29
2.5 2.5 2.5

An Application to Coughs
2 2 2

Correlation Dimension

Correlation Dimension

Correlation Dimension
1.5 1.5 1.5

1 1 1

0.5 0.5 0.5

0 0 0
0.01 0.1 1 0.01 0.1 1 0.01 0.1 1
Disk Radius Disk Radius Disk Radius

File=pos-0421-092-cough-m-53, Delay = 1, Theiler Windows = 50, Gaussian kernel File=pos-0421-093-cough-f-24, Delay = 1, Theiler Windows = 50, Gaussian kernel File=pos-0421-094-cough-m-51, Delay = 1, Theiler Windows = 50, Gaussian kernel
3 3 3
'pos092.plot' using 1:3 'pos093.plot' using 1:3 'pos094.plot' using 1:3

2.5 2.5 2.5

2 2 2

Correlation Dimension

Correlation Dimension

Correlation Dimension
Signal dimension estimation from seven patients tested positive
1.5 1.5 1.5

1 1 1

0.5 0.5 0.5

0 0 0
0.01 0.1 1 0.01 0.1 1 0.01 0.1 1

COVID-19
Disk Radius Disk Radius Disk Radius

1. These are dimension estimates on Positive coughs

 Cough Characterizations
Signal dimension estimation from seven patients tested positive COVID-19

2021-07-29 An Application to Coughs 3

2.5
File=pos-0422-096-cough-m-31, Delay = 1, Theiler Windows = 50, Gaussian kernel

'pos096.plot' using 1:3

Correlation Dimension
1.5

0.5

0
0.01 0.1 1

Signal dimension estimation from seven patients tested positive

Disk Radius

COVID-19
1. These are dimension estimates on Positive coughs
 Cough Characterizations
Size calculation estimation from seven patients tested positive COVID-19
File = pos-0421-084-cough-m-50.dat, Delay = 1, Theiler Windows = 50 File = pos-0421-086-cough-m-65.dat, Delay = 1, Theiler Windows = 50 File = pos-0421-087-cough-f-40.dat, Delay = 1, Theiler Windows = 50
5 8 25
'pos084.cr' u 1:4 'pos086.cr' u 1:4 'pos087.cr' u 1:4

2021-07-29
4 20
6

An Application to Coughs
5
3 15

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Sizes

Sizes
4

2 10
3

2
1 5

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0.01 0.1 1 0.01 0.1 1 0.01 0.1 1
Disk Radius Disk Radius Disk Radius

File = pos-0421-092-cough-m-53.dat, Delay = 1, Theiler Windows = 50 File = pos-0421-093-cough-f-24.dat, Delay = 1, Theiler Windows = 50 File = pos-0421-094-cough-m-51.dat, Delay = 1, Theiler Windows = 50
14 12
100 'pos092.cr' u 1:4 'pos093.cr' u 1:4 'pos094.cr' u 1:4

12
10

80
10
8

Size calculation estimation from seven patients tested positive

60 8

Sizes

Sizes

Sizes
6

6
40
4
4

20
2
2

0 0 0
0.01 0.1 1 0.01 0.1 1 0.01 0.1 1

COVID-19
Disk Radius Disk Radius Disk Radius

1. These are corresponding signal sizes estimated on Positive coughs

 Cough Characterizations
Size calculation estimation from seven patients tested positive COVID-19

2021-07-29 An Application to Coughs 8

7
File = pos-0422-096-cough-m-31.dat, Delay = 1, Theiler Windows = 50

'pos096.cr' u 1:4

Sizes
4

0
0.01 0.1 1

Size calculation estimation from seven patients tested positive

Disk Radius

COVID-19
1. These are corresponding signal sizes estimated on Positive coughs
 Cough Characterizations
Fractal Measurement Results

Sample 083 Sample 084

m
Dim Size Dim Size

2021-07-29 An Application to Coughs

1
2
0.625900
0.772695
2.723572
3.835548
0.538790
0.611182
2.360881
2.656997
3 0.890937 4.893179 0.630288 2.586158
4 0.945543 5.251648 0.664709 2.680730
5 1.005021 5.822704 0.670168 2.487616
6 1.079067 6.707915 0.696175 2.525424
7 1.119844 7.043916 0.713580 2.527889

Fractal Measurement Results 8

9
10
1.156930
1.188630
1.217889
7.415818
7.782917
8.107893
0.715849
0.714913
0.718056
2.433963
2.348750
2.315433
Fractal? No N/A Yes Applicable

1. Not all results are valid. For example, Some numerical results for each m are tabulated in
here For Sample 083, each measurement at embedding dimension m gives a significantly
different D. This suggests that there is no fractality found in the sample. Furthermore,
each number does not equal to corresponding m. So it is not noise either. Both means
the numbers calculated for its size is invalid.
2. In contrast numerical results for Sample 084 confim the existence of fractality at D ≈ 0.7.
As a result, sizes calculation is valid. Averaging all sizes result in a signal size of 2.47 at
dimension 0.70.
 Cough Characterizations
Concluding Remarks

2021-07-29 Concluding Remarks • Fractal characterizations

of Coughs
• Coughs exhibit fractality

Concluding Remarks

1. We have developed a signal processing scheme to characterize coughs based on fractality.

In this preliminary study, we apply our fractal signal size estimator on two samples,
representing coughs coming from persons with negative and positive Covid-19 disease,
respectively. Our hypothesis that COVID disease causes disruptions in the air flow during
coughing, causing fractal behavior into signals.
2. Our results confirm this by showing fractality on samples coming from patient with
positive Covid-19 disease. We need further study with more data, better segmentation
scheme, and adjustment of various sampling related parameters. We believe this scheme
will improve machine learning performance.
3. This result can improve performance of pre-screening for identification the presence
respiratory diseases, such as Covid-19
4. Than you