ML Basics, warming up with small data¶

In [1]:

print(__doc__)

import matplotlib.pyplot as plt
from sklearn import datasets
from sklearn.decomposition import PCA
from sklearn import metrics
import pandas as pd
import seaborn as sns
import numpy as np

Automatically created module for IPython interactive environment

Read poll data¶

In [2]:

dfInit = pd.read_csv(('./Data/MUSA-650WelcomePoll.csv'))
dfInit.head()

Out[2]:

	Timestamp	Q1_General background in data analysis?	Q2_Hands-on experience in data analysis using Python?	Q3_Experience in programming in general?	Q4_General background in machine learning?	Q5_Hands-on experience in running machine learning applications?	Q6_Which one would you prefer on a Sunday afternoon?	Q7_Hands-on experience in image analysis using satellite images?	Q8_Level of interest in mathematics?	Q9_Level of interest in reading?	Q10_Level of stress about this class?	Q11_Your overall motivation about this class?
0	2020/01/14 5:11:10 PM EST	8	5	4	6	7	Running	5	3	5	7	3
1	2020/01/14 5:15:45 PM EST	8	8	5	5	6	Reading	7	7	6	7	8
2	2020/01/14 10:10:14 PM EST	6	6	6	6	5	Watching a movie	7	7	7	7	7
3	2020/01/15 10:02:48 AM EST	5	3	6	4	4	Watching a movie	3	8	8	5	10
4	2020/01/15 10:03:20 AM EST	6	6	5	4	3	Reading	4	5	4	10	8

Calculate relative timestamp¶

In [3]:

dfInit.Timestamp = pd.to_datetime(dfInit.Timestamp, format='%Y/%m/%d %I:%M:%S %p EST')
dfInit['tsRel'] = (dfInit.Timestamp - dfInit.Timestamp.min()).dt.total_seconds()
dfInit[['Timestamp', 'tsRel']].head(10)

Out[3]:

	Timestamp	tsRel
0	2020-01-14 17:11:10	0.0
1	2020-01-14 17:15:45	275.0
2	2020-01-14 22:10:14	17944.0
3	2020-01-15 10:02:48	60698.0
4	2020-01-15 10:03:20	60730.0
5	2020-01-15 10:03:43	60753.0
6	2020-01-15 10:03:50	60760.0
7	2020-01-15 10:03:53	60763.0
8	2020-01-15 10:03:59	60769.0
9	2020-01-15 10:04:03	60773.0

Column names¶

In [4]:

df = dfInit[dfInit.columns[1:]]
initCol = df.columns.tolist()
initCol

Out[4]:

['Q1_General background in data analysis?',
 'Q2_Hands-on experience in data analysis using Python?',
 'Q3_Experience in programming in general?',
 'Q4_General background in machine learning?',
 'Q5_Hands-on experience in running machine learning applications?',
 'Q6_Which one would you prefer on a Sunday afternoon?',
 'Q7_Hands-on experience in image analysis using satellite images?',
 'Q8_Level of interest in mathematics?',
 'Q9_Level of interest in reading?',
 'Q10_Level of stress about this class?',
 'Q11_Your overall motivation about this class?',
 'tsRel']

In [5]:

df.columns = df.columns.str.split('_', 1).str[0].tolist()
df.head()

Out[5]:

	Q1	Q2	Q3	Q4	Q5	Q6	Q7	Q8	Q9	Q10	Q11	tsRel
0	8	5	4	6	7	Running	5	3	5	7	3	0.0
1	8	8	5	5	6	Reading	7	7	6	7	8	275.0
2	6	6	6	6	5	Watching a movie	7	7	7	7	7	17944.0
3	5	3	6	4	4	Watching a movie	3	8	8	5	10	60698.0
4	6	6	5	4	3	Reading	4	5	4	10	8	60730.0

Visualize correlations¶

In [6]:

#sns.pairplot(df, kind = 'reg')

In [7]:

df.corr()

Out[7]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	tsRel
Q1	1.000000	0.766725	0.713877	0.624063	0.738857	0.676150	0.405270	-0.244388	-0.441883	0.042206	0.313668
Q2	0.766725	1.000000	0.639008	0.481836	0.568244	0.692275	0.399874	-0.321784	-0.329991	0.099348	0.383485
Q3	0.713877	0.639008	1.000000	0.564825	0.544057	0.616467	0.596732	-0.083087	-0.631657	0.400580	0.457261
Q4	0.624063	0.481836	0.564825	1.000000	0.945541	0.450752	0.426714	-0.461877	-0.168868	0.036739	0.440323
Q5	0.738857	0.568244	0.544057	0.945541	1.000000	0.444940	0.467669	-0.463201	-0.263556	-0.023930	0.407507
Q7	0.676150	0.692275	0.616467	0.450752	0.444940	1.000000	0.184545	-0.198770	-0.284418	0.045276	0.152171
Q8	0.405270	0.399874	0.596732	0.426714	0.467669	0.184545	1.000000	-0.126656	-0.205698	0.501068	0.036620
Q9	-0.244388	-0.321784	-0.083087	-0.461877	-0.463201	-0.198770	-0.126656	1.000000	-0.217410	0.228420	-0.193531
Q10	-0.441883	-0.329991	-0.631657	-0.168868	-0.263556	-0.284418	-0.205698	-0.217410	1.000000	-0.133846	-0.311850
Q11	0.042206	0.099348	0.400580	0.036739	-0.023930	0.045276	0.501068	0.228420	-0.133846	1.000000	0.430875
tsRel	0.313668	0.383485	0.457261	0.440323	0.407507	0.152171	0.036620	-0.193531	-0.311850	0.430875	1.000000

In [8]:

corr = df.corr()
sns.heatmap(corr, xticklabels=corr.columns, yticklabels=corr.columns)

Out[8]:

<AxesSubplot:>

In [9]:

initCol

Out[9]:

['Q1_General background in data analysis?',
 'Q2_Hands-on experience in data analysis using Python?',
 'Q3_Experience in programming in general?',
 'Q4_General background in machine learning?',
 'Q5_Hands-on experience in running machine learning applications?',
 'Q6_Which one would you prefer on a Sunday afternoon?',
 'Q7_Hands-on experience in image analysis using satellite images?',
 'Q8_Level of interest in mathematics?',
 'Q9_Level of interest in reading?',
 'Q10_Level of stress about this class?',
 'Q11_Your overall motivation about this class?',
 'tsRel']

Handling categorical variables (visualization)¶

In [10]:

sns.catplot(x="Q6", y="Q11", data=df);

Handling categorical variables (Data analysis)¶

In [11]:

df2 = pd.get_dummies(df, columns=['Q6'])

In [12]:

df2

Out[12]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	tsRel	Q6_Reading	Q6_Running	Q6_Watching a movie
0	8	5	4	6	7	5	3	5	7	3	0.0	0	1	0
1	8	8	5	5	6	7	7	6	7	8	275.0	1	0	0
2	6	6	6	6	5	7	7	7	7	7	17944.0	0	0	1
3	5	3	6	4	4	3	8	8	5	10	60698.0	0	0	1
4	6	6	5	4	3	4	5	4	10	8	60730.0	1	0	0
5	8	7	8	3	3	8	4	10	2	8	60753.0	0	1	0
6	4	3	1	1	1	1	1	10	8	8	60760.0	1	0	0
7	7	3	7	6	5	4	6	8	6	9	60763.0	1	0	0
8	5	5	5	4	4	4	4	5	5	7	60769.0	0	0	1
9	6	6	6	6	6	4	6	6	5	6	60773.0	0	0	1
10	4	4	4	5	3	5	2	7	8	7	60783.0	0	0	1
11	7	7	7	2	2	7	6	7	5	8	60790.0	0	1	0
12	8	8	8	6	6	8	7	8	6	8	60800.0	0	0	1
13	4	4	4	1	1	1	5	7	7	8	60801.0	0	0	1
14	8	7	7	7	7	7	10	5	6	10	60812.0	0	1	0
15	7	7	6	6	6	6	6	6	5	7	60817.0	0	0	1
16	7	6	6	5	5	1	7	7	4	7	60823.0	1	0	0
17	6	6	6	5	5	2	9	9	7	9	60939.0	0	0	1
18	9	9	9	9	9	7	6	5	4	10	443956.0	0	0	1

In [13]:

dfTmp = df2[['Q8', 'Q9', 'Q10', 'Q11', 'Q6_Reading', 'Q6_Running', 'Q6_Watching a movie',]].copy()

In [14]:

#sns.pairplot(dfTmp, kind = 'reg')

In [15]:

corr = df.corr()
sns.heatmap(corr, xticklabels=corr.columns, yticklabels=corr.columns)

Out[15]:

<AxesSubplot:>

Dealing with outliers (focusing on tsRel)¶

Visualize data¶

In [16]:

initCol

Out[16]:

['Q1_General background in data analysis?',
 'Q2_Hands-on experience in data analysis using Python?',
 'Q3_Experience in programming in general?',
 'Q4_General background in machine learning?',
 'Q5_Hands-on experience in running machine learning applications?',
 'Q6_Which one would you prefer on a Sunday afternoon?',
 'Q7_Hands-on experience in image analysis using satellite images?',
 'Q8_Level of interest in mathematics?',
 'Q9_Level of interest in reading?',
 'Q10_Level of stress about this class?',
 'Q11_Your overall motivation about this class?',
 'tsRel']

Q: Is there a correlation between how fast a student answered the poll and answers to questions?¶

In [17]:

dfTmp = df[['tsRel','Q3', 'Q10', 'Q11']].copy()
corr = dfTmp.corr()
sns.heatmap(corr, xticklabels=corr.columns, yticklabels=corr.columns)
print(corr['tsRel'])

tsRel    1.000000
Q3       0.457261
Q10     -0.311850
Q11      0.430875
Name: tsRel, dtype: float64

WARNING: Outliers may lead to incorrect conclusions!¶

In [18]:

sns.regplot(x='tsRel', y='Q3', data=dfTmp, color="g")

Out[18]:

<AxesSubplot:xlabel='tsRel', ylabel='Q3'>

In [19]:

sns.distplot(dfTmp.tsRel, hist=True, rug=True, color="g")

/home/guraylab/anaconda3/envs/musa-650/lib/python3.9/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `histplot` (an axes-level function for histograms).
  warnings.warn(msg, FutureWarning)
/home/guraylab/anaconda3/envs/musa-650/lib/python3.9/site-packages/seaborn/distributions.py:2103: FutureWarning: The `axis` variable is no longer used and will be removed. Instead, assign variables directly to `x` or `y`.
  warnings.warn(msg, FutureWarning)

Out[19]:

<AxesSubplot:xlabel='tsRel', ylabel='Density'>

What is an outlier? Let's zoom into the data¶

In [20]:

ax = sns.distplot(dfTmp.tsRel, hist = True, color="g")
ax.set_xlim(0, 100000)
#ax.set_ylim(0, 0.008)

/home/guraylab/anaconda3/envs/musa-650/lib/python3.9/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `histplot` (an axes-level function for histograms).
  warnings.warn(msg, FutureWarning)

Out[20]:

(0.0, 100000.0)

In [21]:

dfTmp.tsRel.median()

Out[21]:

60773.00000000001

In [22]:

dfTmp.tsRel - dfTmp.tsRel.median()

Out[22]:

0     -60773.0
1     -60498.0
2     -42829.0
3        -75.0
4        -43.0
5        -20.0
6        -13.0
7        -10.0
8         -4.0
9          0.0
10        10.0
11        17.0
12        27.0
13        28.0
14        39.0
15        44.0
16        50.0
17       166.0
18    383183.0
Name: tsRel, dtype: float64

In [23]:

dfInit.Timestamp

Out[23]:

0    2020-01-14 17:11:10
1    2020-01-14 17:15:45
2    2020-01-14 22:10:14
3    2020-01-15 10:02:48
4    2020-01-15 10:03:20
5    2020-01-15 10:03:43
6    2020-01-15 10:03:50
7    2020-01-15 10:03:53
8    2020-01-15 10:03:59
9    2020-01-15 10:04:03
10   2020-01-15 10:04:13
11   2020-01-15 10:04:20
12   2020-01-15 10:04:30
13   2020-01-15 10:04:31
14   2020-01-15 10:04:42
15   2020-01-15 10:04:47
16   2020-01-15 10:04:53
17   2020-01-15 10:06:49
18   2020-01-19 20:30:26
Name: Timestamp, dtype: datetime64[ns]

Detect outliers¶

What about using standard scaling (z-score transformation) + thresholding¶

Typical outlier threshold: more than +- 2 std. (z<-2 or z>2)¶

In [24]:

tsRel_z = (dfTmp.tsRel - dfTmp.tsRel.mean()) / dfTmp.tsRel.std()
tsRel_z

Out[24]:

0    -0.783125
1    -0.780147
2    -0.588803
3    -0.125805
4    -0.125459
5    -0.125209
6    -0.125134
7    -0.125101
8    -0.125036
9    -0.124993
10   -0.124885
11   -0.124809
12   -0.124700
13   -0.124690
14   -0.124571
15   -0.124516
16   -0.124451
17   -0.123195
18    4.024628
Name: tsRel, dtype: float64

Outlier detection is a serious task!¶

SciKit methods¶

Example: a more advanced outlier detection¶

In [25]:

from sklearn.neighbors import LocalOutlierFactor

# fit the model for outlier detection (default)
X = np.array(dfTmp.tsRel).reshape(dfTmp.shape[0],1)
X.shape
clf = LocalOutlierFactor(n_neighbors=5, contamination=0.1)
clf.fit_predict(X)
dfTmp['outScore'] = clf.negative_outlier_factor_.tolist()
dfTmp

Out[25]:

	tsRel	Q3	Q10	Q11	outScore
0	0.0	4	7	3	-971.093118
1	275.0	5	7	8	-969.221765
2	17944.0	6	7	7	-848.985675
3	60698.0	6	5	10	-2.550890
4	60730.0	5	10	8	-1.646488
5	60753.0	8	2	8	-1.071656
6	60760.0	1	8	8	-0.988349
7	60763.0	7	6	9	-0.988349
8	60769.0	5	5	7	-1.012356
9	60773.0	6	5	6	-1.025628
10	60783.0	4	8	7	-0.890923
11	60790.0	7	5	8	-0.915438
12	60800.0	8	6	8	-1.035467
13	60801.0	4	7	8	-1.023812
14	60812.0	7	6	10	-1.085007
15	60817.0	6	5	7	-1.085007
16	60823.0	6	4	7	-1.194836
17	60939.0	6	7	9	-5.640073
18	443956.0	9	4	10	-13811.188253

In [26]:

dfTmp.plot.scatter(x='tsRel', y='outScore', c='DarkBlue')

Out[26]:

<AxesSubplot:xlabel='tsRel', ylabel='outScore'>

Correlations for filtered data¶

In [27]:

dfTmpFil = dfTmp[np.logical_and(dfTmp.outScore>-5, dfTmp.outScore<5)]
dfTmpFil

Out[27]:

	tsRel	Q3	Q10	Q11	outScore
3	60698.0	6	5	10	-2.550890
4	60730.0	5	10	8	-1.646488
5	60753.0	8	2	8	-1.071656
6	60760.0	1	8	8	-0.988349
7	60763.0	7	6	9	-0.988349
8	60769.0	5	5	7	-1.012356
9	60773.0	6	5	6	-1.025628
10	60783.0	4	8	7	-0.890923
11	60790.0	7	5	8	-0.915438
12	60800.0	8	6	8	-1.035467
13	60801.0	4	7	8	-1.023812
14	60812.0	7	6	10	-1.085007
15	60817.0	6	5	7	-1.085007
16	60823.0	6	4	7	-1.194836

In [28]:

sns.distplot(dfTmpFil.tsRel, hist = True, color="g")

/home/guraylab/anaconda3/envs/musa-650/lib/python3.9/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `histplot` (an axes-level function for histograms).
  warnings.warn(msg, FutureWarning)

Out[28]:

<AxesSubplot:xlabel='tsRel', ylabel='Density'>

In [29]:

corr = dfTmpFil.corr()
sns.heatmap(corr, xticklabels=corr.columns, yticklabels=corr.columns)
print(corr['tsRel'])

tsRel       1.000000
Q3          0.130838
Q10        -0.163241
Q11        -0.344576
outScore    0.702471
Name: tsRel, dtype: float64

In [30]:

sns.regplot(x='tsRel', y='Q3', data=dfTmpFil, color="g")

Out[30]:

<AxesSubplot:xlabel='tsRel', ylabel='Q3'>

In [31]:

df

Out[31]:

	Q1	Q2	Q3	Q4	Q5	Q6	Q7	Q8	Q9	Q10	Q11	tsRel
0	8	5	4	6	7	Running	5	3	5	7	3	0.0
1	8	8	5	5	6	Reading	7	7	6	7	8	275.0
2	6	6	6	6	5	Watching a movie	7	7	7	7	7	17944.0
3	5	3	6	4	4	Watching a movie	3	8	8	5	10	60698.0
4	6	6	5	4	3	Reading	4	5	4	10	8	60730.0
5	8	7	8	3	3	Running	8	4	10	2	8	60753.0
6	4	3	1	1	1	Reading	1	1	10	8	8	60760.0
7	7	3	7	6	5	Reading	4	6	8	6	9	60763.0
8	5	5	5	4	4	Watching a movie	4	4	5	5	7	60769.0
9	6	6	6	6	6	Watching a movie	4	6	6	5	6	60773.0
10	4	4	4	5	3	Watching a movie	5	2	7	8	7	60783.0
11	7	7	7	2	2	Running	7	6	7	5	8	60790.0
12	8	8	8	6	6	Watching a movie	8	7	8	6	8	60800.0
13	4	4	4	1	1	Watching a movie	1	5	7	7	8	60801.0
14	8	7	7	7	7	Running	7	10	5	6	10	60812.0
15	7	7	6	6	6	Watching a movie	6	6	6	5	7	60817.0
16	7	6	6	5	5	Reading	1	7	7	4	7	60823.0
17	6	6	6	5	5	Watching a movie	2	9	9	7	9	60939.0
18	9	9	9	9	9	Watching a movie	7	6	5	4	10	443956.0

Dimensionality reduction¶

In [32]:

mdlPCA = PCA(n_components=5)
XPCA = mdlPCA.fit_transform(df2)

print(mdlPCA.explained_variance_ratio_)
print(np.sum(mdlPCA.explained_variance_ratio_))
plt.plot(np.arange(0,mdlPCA.explained_variance_ratio_.shape[0]), mdlPCA.explained_variance_ratio_, '-ro')

[9.99999996e-01 1.81226177e-09 6.72112392e-10 5.91733094e-10
 3.30434976e-10]
0.9999999994658001

Out[32]:

[<matplotlib.lines.Line2D at 0x7f8fb3069bb0>]

In [33]:

print(mdlPCA.components_[0,:])
plt.plot(np.arange(0,mdlPCA.components_[0,:].shape[0]), mdlPCA.components_[0,:], '-ro')

[ 5.23403869e-06  7.40036105e-06  8.97709992e-06  9.61319140e-06
  9.32793474e-06  3.94503126e-06  8.95009702e-07 -3.58017421e-06
 -6.06213801e-06  7.55257058e-06  1.00000000e+00 -7.70261980e-07
 -6.96515391e-07  1.46677737e-06]

Out[33]:

[<matplotlib.lines.Line2D at 0x7f8fb2fd4e80>]

Question: What is "wrong" in the data?¶

In [34]:

df2.describe()

Out[34]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	tsRel	Q6_Reading	Q6_Running	Q6_Watching a movie
count	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000
mean	6.473684	5.789474	5.789474	4.789474	4.631579	4.789474	5.736842	6.842105	6.000000	7.789474	72315.052632	0.263158	0.210526	0.526316
std	1.540866	1.781976	1.812884	2.016018	2.113726	2.393949	2.256893	1.708253	1.795055	1.618605	92341.691330	0.452414	0.418854	0.512989
min	4.000000	3.000000	1.000000	1.000000	1.000000	1.000000	1.000000	4.000000	2.000000	3.000000	0.000000	0.000000	0.000000	0.000000
25%	5.500000	4.500000	5.000000	4.000000	3.000000	3.500000	4.500000	5.500000	5.000000	7.000000	60741.500000	0.000000	0.000000	0.000000
50%	7.000000	6.000000	6.000000	5.000000	5.000000	5.000000	6.000000	7.000000	6.000000	8.000000	60773.000000	0.000000	0.000000	1.000000
75%	8.000000	7.000000	7.000000	6.000000	6.000000	7.000000	7.000000	8.000000	7.000000	8.500000	60806.500000	0.500000	0.000000	1.000000
max	9.000000	9.000000	9.000000	9.000000	9.000000	8.000000	10.000000	10.000000	10.000000	10.000000	443956.000000	1.000000	1.000000	1.000000

Let's normalize the data¶

In [35]:

df2_norm = (df2-df2.min())/(df2.max()-df2.min())

In [36]:

df2_norm.head()

Out[36]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	tsRel	Q6_Reading	Q6_Running	Q6_Watching a movie
0	0.8	0.333333	0.375	0.625	0.750	0.571429	0.222222	0.166667	0.625	0.000000	0.000000	0.0	1.0	0.0
1	0.8	0.833333	0.500	0.500	0.625	0.857143	0.666667	0.333333	0.625	0.714286	0.000619	1.0	0.0	0.0
2	0.4	0.500000	0.625	0.625	0.500	0.857143	0.666667	0.500000	0.625	0.571429	0.040418	0.0	0.0	1.0
3	0.2	0.000000	0.625	0.375	0.375	0.285714	0.777778	0.666667	0.375	1.000000	0.136721	0.0	0.0	1.0
4	0.4	0.500000	0.500	0.375	0.250	0.428571	0.444444	0.000000	1.000	0.714286	0.136793	1.0	0.0	0.0

In [37]:

df2_norm.describe()

Out[37]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	tsRel	Q6_Reading	Q6_Running	Q6_Watching a movie
count	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000	19.000000
mean	0.494737	0.464912	0.598684	0.473684	0.453947	0.541353	0.526316	0.473684	0.500000	0.684211	0.162888	0.263158	0.210526	0.526316
std	0.308173	0.296996	0.226611	0.252002	0.264216	0.341993	0.250766	0.284709	0.224382	0.231229	0.207997	0.452414	0.418854	0.512989
min	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000
25%	0.300000	0.250000	0.500000	0.375000	0.250000	0.357143	0.388889	0.250000	0.375000	0.571429	0.136819	0.000000	0.000000	0.000000
50%	0.600000	0.500000	0.625000	0.500000	0.500000	0.571429	0.555556	0.500000	0.500000	0.714286	0.136890	0.000000	0.000000	1.000000
75%	0.800000	0.666667	0.750000	0.625000	0.625000	0.857143	0.666667	0.666667	0.625000	0.785714	0.136965	0.500000	0.000000	1.000000
max	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000

In [38]:

mdlPCA = PCA(n_components=5)
XPCA = mdlPCA.fit_transform(df2_norm)

print(mdlPCA.explained_variance_ratio_)
print(np.sum(mdlPCA.explained_variance_ratio_))

plt.plot(np.arange(0,mdlPCA.explained_variance_ratio_.shape[0]), mdlPCA.explained_variance_ratio_, '-ro')

[0.31431827 0.29012089 0.15348486 0.07788586 0.04541328]
0.8812231522564272

Out[38]:

[<matplotlib.lines.Line2D at 0x7f8fb2f5d070>]

In [39]:

print(mdlPCA.components_[0,:])
plt.plot(np.arange(0,mdlPCA.components_[0,:].shape[0]), mdlPCA.components_[0,:], '-ro')

[-0.28489905 -0.3141605  -0.26107415 -0.25405393 -0.27500032 -0.36871538
 -0.17301488  0.12875075  0.16485422 -0.03296608 -0.13459097  0.4957779
 -0.16340968 -0.33236822]

Out[39]:

[<matplotlib.lines.Line2D at 0x7f8fb2f3cac0>]

Remove tsRel column¶

In [40]:

df2_noTs = df2_norm[df2_norm.columns[df2_norm.columns.str.contains('tsRel')==False]]
df2_noTs.head()

Out[40]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	Q6_Reading	Q6_Running	Q6_Watching a movie
0	0.8	0.333333	0.375	0.625	0.750	0.571429	0.222222	0.166667	0.625	0.000000	0.0	1.0	0.0
1	0.8	0.833333	0.500	0.500	0.625	0.857143	0.666667	0.333333	0.625	0.714286	1.0	0.0	0.0
2	0.4	0.500000	0.625	0.625	0.500	0.857143	0.666667	0.500000	0.625	0.571429	0.0	0.0	1.0
3	0.2	0.000000	0.625	0.375	0.375	0.285714	0.777778	0.666667	0.375	1.000000	0.0	0.0	1.0
4	0.4	0.500000	0.500	0.375	0.250	0.428571	0.444444	0.000000	1.000	0.714286	1.0	0.0	0.0

In [41]:

df2_noTs = df2_norm.drop(columns=['tsRel'])
df2_noTs.head()

Out[41]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	Q6_Reading	Q6_Running	Q6_Watching a movie
0	0.8	0.333333	0.375	0.625	0.750	0.571429	0.222222	0.166667	0.625	0.000000	0.0	1.0	0.0
1	0.8	0.833333	0.500	0.500	0.625	0.857143	0.666667	0.333333	0.625	0.714286	1.0	0.0	0.0
2	0.4	0.500000	0.625	0.625	0.500	0.857143	0.666667	0.500000	0.625	0.571429	0.0	0.0	1.0
3	0.2	0.000000	0.625	0.375	0.375	0.285714	0.777778	0.666667	0.375	1.000000	0.0	0.0	1.0
4	0.4	0.500000	0.500	0.375	0.250	0.428571	0.444444	0.000000	1.000	0.714286	1.0	0.0	0.0

In [42]:

mdlPCA = PCA(n_components=5)
XPCA = mdlPCA.fit_transform(df2_noTs)

print(mdlPCA.explained_variance_ratio_)
print(np.sum(mdlPCA.explained_variance_ratio_))

plt.plot(np.arange(0,mdlPCA.explained_variance_ratio_.shape[0]), mdlPCA.explained_variance_ratio_, '-ro')

[0.31894549 0.29885772 0.1547158  0.07966809 0.04678632]
0.898973407637008

Out[42]:

[<matplotlib.lines.Line2D at 0x7f8fb2ea4910>]

In [43]:

print(mdlPCA.components_[0,:])
plt.plot(np.arange(0,mdlPCA.components_[0,:].shape[0]), mdlPCA.components_[0,:], '-ro')

[-0.30244657 -0.32214438 -0.26410732 -0.25227651 -0.27659662 -0.3869891
 -0.17634825  0.12991123  0.1677439  -0.02453888  0.49300779 -0.20299601
 -0.29001178]

Out[43]:

[<matplotlib.lines.Line2D at 0x7f8fb2e8f640>]

Alternative approach: Keep tsRel, but exclude outliers¶

In [44]:

df2Fil = df2[np.logical_and(df2.tsRel>60000, df2.tsRel<61000)]
df2Fil_norm = (df2Fil-df2Fil.min())/(df2Fil.max()-df2Fil.min())
df2Fil_norm.head()

Out[44]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	tsRel	Q6_Reading	Q6_Running	Q6_Watching a movie
3	0.25	0.0	0.714286	0.500000	0.500000	0.285714	0.777778	0.666667	0.375	1.00	0.000000	0.0	0.0	1.0
4	0.50	0.6	0.571429	0.500000	0.333333	0.428571	0.444444	0.000000	1.000	0.50	0.132780	1.0	0.0	0.0
5	1.00	0.8	1.000000	0.333333	0.333333	1.000000	0.333333	1.000000	0.000	0.50	0.228216	0.0	1.0	0.0
6	0.00	0.0	0.000000	0.000000	0.000000	0.000000	0.000000	1.000000	0.750	0.50	0.257261	1.0	0.0	0.0
7	0.75	0.0	0.857143	0.833333	0.666667	0.428571	0.555556	0.666667	0.500	0.75	0.269710	1.0	0.0	0.0

In [45]:

mdlPCA = PCA(n_components=5)
XPCA = mdlPCA.fit_transform(df2Fil_norm)

print(mdlPCA.explained_variance_ratio_)
print(np.sum(mdlPCA.explained_variance_ratio_))

plt.plot(np.arange(0,mdlPCA.explained_variance_ratio_.shape[0]), mdlPCA.explained_variance_ratio_, '-ro')

[0.34631596 0.27017825 0.14469026 0.07712654 0.05616314]
0.8944741480656596

Out[45]:

[<matplotlib.lines.Line2D at 0x7f8fb2dfd2b0>]

In [46]:

print(mdlPCA.components_[0,:])
plt.plot(np.arange(0,mdlPCA.components_[0,:].shape[0]), mdlPCA.components_[0,:], '-ro')

[-0.43656834 -0.36520933 -0.30003171 -0.22317841 -0.26032745 -0.38821589
 -0.21312891  0.05576004  0.17168435 -0.07017853 -0.05979342  0.27181642
 -0.3812503   0.10943387]

Out[46]:

[<matplotlib.lines.Line2D at 0x7f8fb2d60880>]

Predictive models¶

Can we predict motivation?¶

Can we predict stress?¶

In [47]:

df3 = df2.drop(columns=['tsRel'])
df3_norm = (df3-df3.min())/(df3.max()-df3.min())
df3_norm.head()

Out[47]:

	Q1	Q2	Q3	Q4	Q5	Q7	Q8	Q9	Q10	Q11	Q6_Reading	Q6_Running	Q6_Watching a movie
0	0.8	0.333333	0.375	0.625	0.750	0.571429	0.222222	0.166667	0.625	0.000000	0.0	1.0	0.0
1	0.8	0.833333	0.500	0.500	0.625	0.857143	0.666667	0.333333	0.625	0.714286	1.0	0.0	0.0
2	0.4	0.500000	0.625	0.625	0.500	0.857143	0.666667	0.500000	0.625	0.571429	0.0	0.0	1.0
3	0.2	0.000000	0.625	0.375	0.375	0.285714	0.777778	0.666667	0.375	1.000000	0.0	0.0	1.0
4	0.4	0.500000	0.500	0.375	0.250	0.428571	0.444444	0.000000	1.000	0.714286	1.0	0.0	0.0

Select X and y¶

In [48]:

colX = df3.columns[pd.np.r_[0:8,10:13]]
colX.tolist()

/tmp/ipykernel_1809247/2650173780.py:1: FutureWarning: The pandas.np module is deprecated and will be removed from pandas in a future version. Import numpy directly instead
  colX = df3.columns[pd.np.r_[0:8,10:13]]

Out[48]:

['Q1',
 'Q2',
 'Q3',
 'Q4',
 'Q5',
 'Q7',
 'Q8',
 'Q9',
 'Q6_Reading',
 'Q6_Running',
 'Q6_Watching a movie']

In [49]:

colY = ['Q10']  # level of stress;
colY = ['Q11']  # level of motivation;

colY

Out[49]:

['Q11']

In [50]:

X = np.array(df3[colX])
print(X.shape)
X

(19, 11)

Out[50]:

array([[ 8,  5,  4,  6,  7,  5,  3,  5,  0,  1,  0],
       [ 8,  8,  5,  5,  6,  7,  7,  6,  1,  0,  0],
       [ 6,  6,  6,  6,  5,  7,  7,  7,  0,  0,  1],
       [ 5,  3,  6,  4,  4,  3,  8,  8,  0,  0,  1],
       [ 6,  6,  5,  4,  3,  4,  5,  4,  1,  0,  0],
       [ 8,  7,  8,  3,  3,  8,  4, 10,  0,  1,  0],
       [ 4,  3,  1,  1,  1,  1,  1, 10,  1,  0,  0],
       [ 7,  3,  7,  6,  5,  4,  6,  8,  1,  0,  0],
       [ 5,  5,  5,  4,  4,  4,  4,  5,  0,  0,  1],
       [ 6,  6,  6,  6,  6,  4,  6,  6,  0,  0,  1],
       [ 4,  4,  4,  5,  3,  5,  2,  7,  0,  0,  1],
       [ 7,  7,  7,  2,  2,  7,  6,  7,  0,  1,  0],
       [ 8,  8,  8,  6,  6,  8,  7,  8,  0,  0,  1],
       [ 4,  4,  4,  1,  1,  1,  5,  7,  0,  0,  1],
       [ 8,  7,  7,  7,  7,  7, 10,  5,  0,  1,  0],
       [ 7,  7,  6,  6,  6,  6,  6,  6,  0,  0,  1],
       [ 7,  6,  6,  5,  5,  1,  7,  7,  1,  0,  0],
       [ 6,  6,  6,  5,  5,  2,  9,  9,  0,  0,  1],
       [ 9,  9,  9,  9,  9,  7,  6,  5,  0,  0,  1]])

In [51]:

y = np.array(df3[colY])
print(y.shape)
y

(19, 1)

Out[51]:

array([[ 3],
       [ 8],
       [ 7],
       [10],
       [ 8],
       [ 8],
       [ 8],
       [ 9],
       [ 7],
       [ 6],
       [ 7],
       [ 8],
       [ 8],
       [ 8],
       [10],
       [ 7],
       [ 7],
       [ 9],
       [10]])

Normalize data¶

In [52]:

from sklearn.preprocessing import StandardScaler
from sklearn.preprocessing import MinMaxScaler

#scaler = StandardScaler()
scaler = MinMaxScaler()

scaler.fit(X)
Xnorm = scaler.transform(X)
Xnorm.max(axis=0)

Out[52]:

array([1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.])

In [53]:

import numpy as np
from sklearn.svm import SVR
import matplotlib.pyplot as plt

Cross validation with leave one out¶

In [54]:

from sklearn.model_selection import LeaveOneOut

loo = LeaveOneOut()
for train_index, test_index in loo.split(Xnorm):
    print('TRAIN: ' + str(train_index) + '  TEST: ' +  str(test_index))

TRAIN: [ 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18]  TEST: [0]
TRAIN: [ 0  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18]  TEST: [1]
TRAIN: [ 0  1  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18]  TEST: [2]
TRAIN: [ 0  1  2  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18]  TEST: [3]
TRAIN: [ 0  1  2  3  5  6  7  8  9 10 11 12 13 14 15 16 17 18]  TEST: [4]
TRAIN: [ 0  1  2  3  4  6  7  8  9 10 11 12 13 14 15 16 17 18]  TEST: [5]
TRAIN: [ 0  1  2  3  4  5  7  8  9 10 11 12 13 14 15 16 17 18]  TEST: [6]
TRAIN: [ 0  1  2  3  4  5  6  8  9 10 11 12 13 14 15 16 17 18]  TEST: [7]
TRAIN: [ 0  1  2  3  4  5  6  7  9 10 11 12 13 14 15 16 17 18]  TEST: [8]
TRAIN: [ 0  1  2  3  4  5  6  7  8 10 11 12 13 14 15 16 17 18]  TEST: [9]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 11 12 13 14 15 16 17 18]  TEST: [10]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 12 13 14 15 16 17 18]  TEST: [11]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 11 13 14 15 16 17 18]  TEST: [12]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 14 15 16 17 18]  TEST: [13]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 15 16 17 18]  TEST: [14]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 16 17 18]  TEST: [15]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 17 18]  TEST: [16]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 18]  TEST: [17]
TRAIN: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17]  TEST: [18]

In [55]:

import warnings
warnings.filterwarnings('ignore')

from sklearn.svm import LinearSVR

loo = LeaveOneOut()

predAll = np.zeros([y.shape[0],1])

i=0
for train_index, test_index in loo.split(Xnorm):

    X_train, X_test = Xnorm[train_index], Xnorm[test_index]
    y_train, y_test = y[train_index], y[test_index]

    regr = LinearSVR(random_state=0, tol=1e-5)
    
    regr.fit(X_train, y_train)  #  Train the model

    ypred = regr.predict(X_test)  #  Apply the model
    
    predAll[i] = ypred
    
    print('Y : ' + str(y_test) + ' , pred as: ' + str(ypred))
    i = i + 1 

Y : [[3]] , pred as: [6.71770473]
Y : [[8]] , pred as: [8.44358673]
Y : [[7]] , pred as: [8.57175498]
Y : [[10]] , pred as: [7.62213136]
Y : [[8]] , pred as: [6.70446542]
Y : [[8]] , pred as: [8.9269527]
Y : [[8]] , pred as: [5.14777884]
Y : [[9]] , pred as: [8.02397316]
Y : [[7]] , pred as: [6.22595715]
Y : [[6]] , pred as: [7.94496256]
Y : [[7]] , pred as: [6.21621235]
Y : [[8]] , pred as: [7.00076291]
Y : [[8]] , pred as: [9.45348764]
Y : [[8]] , pred as: [6.27163448]
Y : [[10]] , pred as: [6.519619]
Y : [[7]] , pred as: [8.10618284]
Y : [[7]] , pred as: [8.58400087]
Y : [[9]] , pred as: [7.92971992]
Y : [[10]] , pred as: [6.78948034]

In [56]:

np.corrcoef(y.T, predAll.T)

Out[56]:

array([[1.        , 0.01086243],
       [0.01086243, 1.        ]])

In [57]:

plt.scatter(y.T, predAll.T)

Out[57]:

<matplotlib.collections.PathCollection at 0x7f8fb2cd9040>