$k$-NN's: $k$-Nearest Neighbours¶

variationalform https://variationalform.github.io/¶

Just Enough: progress at pace¶

https://variationalform.github.io/

https://github.com/variationalform

https://www.brunel.ac.uk/people/simon-shaw.

This work is licensed under CC BY-SA 4.0 (Attribution-ShareAlike 4.0 International)

Visit http://creativecommons.org/licenses/by-sa/4.0/ to see the terms.

This document uses python and also makes use of LaTeX in Markdown

What this is about:¶

You will be introduced to ...

  • The penguins data set, data frames, data selection
  • Data engineering: mean imputation, and dropping unknowns
  • Data bifurcation and trifurcation; calibration; tuning and hyperparameters
  • $k$-Nearest Neighbours - classifying by nearness
  • using the KNeighborsClassifier from sklearn.neighbors
  • Confusion Matrices

The idea is that by using vectors to represent our data set, we can classify a new data point by finding the nearest data point to it for which the class is known. We then assign the new point with the same class.

As usual our emphasis will be on doing rather than proving: just enough: progress at pace.

Assigned Reading¶

For this worksheet you should read pages 19 - 25 of

  • MLFCES: Machine Learning: A First Course for Engineers and Scientists, by Andreas Lindholm, Niklas Wahlström, Fredrik Lindsten, Thomas B. Schön. Cambridge University Press. http://smlbook.org.

The pages leading up to Page 19 are also highly recommended as an overview of concepts, purpose and uses of Machine Learning.

Penguins: An Example Data Set¶

We bring in our standard imports and then recall the data sets that are available in seaborn. We'll be using the penguins data.

In [1]:
import matplotlib.pyplot as plt
import numpy as np
from sklearn import datasets, linear_model
import pandas as pd
import seaborn as sns
In [2]:
# See, for example,
#   https://github.com/mwaskom/seaborn-data
#   https://blog.enterprisedna.co/how-to-load-sample-datasets-in-python/
sns.get_dataset_names()
Out[2]:
['anagrams',
 'anscombe',
 'attention',
 'brain_networks',
 'car_crashes',
 'diamonds',
 'dots',
 'dowjones',
 'exercise',
 'flights',
 'fmri',
 'geyser',
 'glue',
 'healthexp',
 'iris',
 'mpg',
 'penguins',
 'planets',
 'seaice',
 'taxis',
 'tips',
 'titanic']

Some Data-Engineering¶

As we have seen, there are a lot of data sets here that can be used to demonstrate various aspects of, and techniques in, Machine Learning and Data Science, and we'll look at a few of them - and others - as we progress.

To start with though we'll be working with the penguins data set. Before we do any machine learning we are going to have to do some data cleaning, see e.g. https://en.wikipedia.org/wiki/Data_cleansing, to remove some undefined values.

This shouldn't be confused with https://en.wikipedia.org/wiki/Feature_engineering.

Let's grab the penguins data and see what is in it. We load it into a data frame called dfp, as in data frame for penguins, and then look at the head of the table - the first few rows.

In [3]:
dfp = sns.load_dataset('penguins')
dfp.head()
Out[3]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
0 Adelie Torgersen 39.1 18.7 181.0 3750.0 Male
1 Adelie Torgersen 39.5 17.4 186.0 3800.0 Female
2 Adelie Torgersen 40.3 18.0 195.0 3250.0 Female
3 Adelie Torgersen NaN NaN NaN NaN NaN
4 Adelie Torgersen 36.7 19.3 193.0 3450.0 Female

Let's look at the shape of the data set - how many rows and columns does it have?

In [4]:
num_rows, num_columns = dfp.shape
print('number of data points (or observations) = ', num_rows)
print('number of features (or measurement) = ', num_columns)

number of data points (or observations) =  344
number of features (or measurement) =  7

So, the data set contains 344 rows and seven columns. Each row corresponds to a single penguin, and for each row each column corresponds to a feature of that penguin. We can see its species, the island it was found on, its bill length, bill depth, and flipper length - all in millimetres, its body mass in grams, and its gender.

We can also see NaN values in row 3. That's the fourth row - be careful of this, indexing starts at zero. This stands for Not a Number and means that we can't use those values as they stand. We don't know why they are there - paerhaps the data got corrupted. It's a fact of life though that data sets are often a bit messy with wrong, missing or corrupted values. We'll see a couple of ways to deal with these instances below.

We haven't listed every row - just the head of the data table. Another way to visualize these data is to use a scatter plot.

See e.g. https://seaborn.pydata.org/generated/seaborn.scatterplot.html

In [5]:
sns.scatterplot(data=dfp, x="body_mass_g", y="bill_depth_mm", hue="species", style="sex")
Out[5]:
<AxesSubplot:xlabel='body_mass_g', ylabel='bill_depth_mm'>

If that looks a little cramped you can control the size like this:

In [6]:
plt.figure(figsize=(8, 8))
sns.scatterplot(data=dfp, x="body_mass_g", y="bill_depth_mm", hue="island")
Out[6]:
<AxesSubplot:xlabel='body_mass_g', ylabel='bill_depth_mm'>

When we issued the command dfp.head() above we got to see the top of the table. We can also see the bottom like this:

In [7]:
dfp.tail()
Out[7]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
339 Gentoo Biscoe NaN NaN NaN NaN NaN
340 Gentoo Biscoe 46.8 14.3 215.0 4850.0 Female
341 Gentoo Biscoe 50.4 15.7 222.0 5750.0 Male
342 Gentoo Biscoe 45.2 14.8 212.0 5200.0 Female
343 Gentoo Biscoe 49.9 16.1 213.0 5400.0 Male

This has given us two species, Adelie and Gentoo, but from the plots above we know there is also a third: Chinstrap.

We can also see from the head and tail functions that there are two islands, Torgersen and Biscoe, and that - from the plots - there is a third, Dream.

How could we find these without having to plot the data? Well, we could look at the whole table with this command:

print(dfp.to_string())

Try it in the cell below - uncomment it and execute the cell. It's a bit messy (and what if we had millions of rows?).

Now re-comment it and execute the cell again to clear that very long output.

In [8]:
# print(dfp.to_string())

A simpler way is to ask for all the unique entries in the species column, and
in the island column:

In [9]:
dfp.species.unique()
Out[9]:
array(['Adelie', 'Chinstrap', 'Gentoo'], dtype=object)
In [10]:
dfp.island.unique()
Out[10]:
array(['Torgersen', 'Biscoe', 'Dream'], dtype=object)

Summary¶

We have seen that three species are documented on three Antarctic islands.

We have also seen that some values are undefined: NaN stands for Not a Number. This may indicate that the data was not captured reliably.

We can see how many rows contain undefined values with this command:

In [11]:
dfp.isna().sum()
Out[11]:
species               0
island                0
bill_length_mm        2
bill_depth_mm         2
flipper_length_mm     2
body_mass_g           2
sex                  11
dtype: int64

There are at least eleven - and there could be 11+2+2+2+2. Let's find them.

In the following axis=1 tells python that we want to find rows with NaN in, as opposed to columns.

In [12]:
dfp[dfp.isna().any(axis=1)]
Out[12]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
3 Adelie Torgersen NaN NaN NaN NaN NaN
8 Adelie Torgersen 34.1 18.1 193.0 3475.0 NaN
9 Adelie Torgersen 42.0 20.2 190.0 4250.0 NaN
10 Adelie Torgersen 37.8 17.1 186.0 3300.0 NaN
11 Adelie Torgersen 37.8 17.3 180.0 3700.0 NaN
47 Adelie Dream 37.5 18.9 179.0 2975.0 NaN
246 Gentoo Biscoe 44.5 14.3 216.0 4100.0 NaN
286 Gentoo Biscoe 46.2 14.4 214.0 4650.0 NaN
324 Gentoo Biscoe 47.3 13.8 216.0 4725.0 NaN
336 Gentoo Biscoe 44.5 15.7 217.0 4875.0 NaN
339 Gentoo Biscoe NaN NaN NaN NaN NaN

We can get a list of the row index numbers like this:

In [13]:
NaN_rows = dfp[dfp.isna().any(axis=1)]
print(NaN_rows.index)

Int64Index([3, 8, 9, 10, 11, 47, 246, 286, 324, 336, 339], dtype='int64')

And we can use these as an alternative to the axis=1 command above:

In [14]:
dfp.loc[NaN_rows.index]
Out[14]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
3 Adelie Torgersen NaN NaN NaN NaN NaN
8 Adelie Torgersen 34.1 18.1 193.0 3475.0 NaN
9 Adelie Torgersen 42.0 20.2 190.0 4250.0 NaN
10 Adelie Torgersen 37.8 17.1 186.0 3300.0 NaN
11 Adelie Torgersen 37.8 17.3 180.0 3700.0 NaN
47 Adelie Dream 37.5 18.9 179.0 2975.0 NaN
246 Gentoo Biscoe 44.5 14.3 216.0 4100.0 NaN
286 Gentoo Biscoe 46.2 14.4 214.0 4650.0 NaN
324 Gentoo Biscoe 47.3 13.8 216.0 4725.0 NaN
336 Gentoo Biscoe 44.5 15.7 217.0 4875.0 NaN
339 Gentoo Biscoe NaN NaN NaN NaN NaN

Data Engineering - our first method¶

One way to deal with missing values like this is to simply fill them with 'reasonable' values. For example, we can replace the numerical values with the mean, or average, of that feature, and replace categorical values with just one of the possible categories.

For example, let's use the mean for numerical values and treat all missing genders as Female.

In [15]:
# from https://datagy.io/pandas-fillna/
dfp1 = dfp.fillna({'bill_length_mm'   : dfp['bill_length_mm'].mean(),
                   'bill_depth_mm'    : dfp['bill_depth_mm'].mean(),
                   'flipper_length_mm': dfp['flipper_length_mm'].mean(),
                   'body_mass_g'      : dfp['body_mass_g'].mean(),
                   'sex': 'Female'})

Mean Imputation¶

Replacing a missing numerical feature value with the mean of the known feature values in this way is called imputing the mean. It is easy to implement - just one line above - but you should be aware that it corrupts the original data set.

  • On the upside this process maintains the sample size
  • On the downside it (probably) alters some statistical properties of the data (the unknown variance, for example).

As an analyst you would be responsible for taking a decision as to how to deal with missing values. You may not be the only one involved in that decision.

We can compare the old and new data frames just to check this worked as expected.

In [16]:
# Here is the new one with the NaN's replaced - or engineered out
dfp1.loc[NaN_rows.index]
Out[16]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
3 Adelie Torgersen 43.92193 17.15117 200.915205 4201.754386 Female
8 Adelie Torgersen 34.10000 18.10000 193.000000 3475.000000 Female
9 Adelie Torgersen 42.00000 20.20000 190.000000 4250.000000 Female
10 Adelie Torgersen 37.80000 17.10000 186.000000 3300.000000 Female
11 Adelie Torgersen 37.80000 17.30000 180.000000 3700.000000 Female
47 Adelie Dream 37.50000 18.90000 179.000000 2975.000000 Female
246 Gentoo Biscoe 44.50000 14.30000 216.000000 4100.000000 Female
286 Gentoo Biscoe 46.20000 14.40000 214.000000 4650.000000 Female
324 Gentoo Biscoe 47.30000 13.80000 216.000000 4725.000000 Female
336 Gentoo Biscoe 44.50000 15.70000 217.000000 4875.000000 Female
339 Gentoo Biscoe 43.92193 17.15117 200.915205 4201.754386 Female
In [17]:
# Here is the old one with the NaN's
dfp.loc[NaN_rows.index]
Out[17]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
3 Adelie Torgersen NaN NaN NaN NaN NaN
8 Adelie Torgersen 34.1 18.1 193.0 3475.0 NaN
9 Adelie Torgersen 42.0 20.2 190.0 4250.0 NaN
10 Adelie Torgersen 37.8 17.1 186.0 3300.0 NaN
11 Adelie Torgersen 37.8 17.3 180.0 3700.0 NaN
47 Adelie Dream 37.5 18.9 179.0 2975.0 NaN
246 Gentoo Biscoe 44.5 14.3 216.0 4100.0 NaN
286 Gentoo Biscoe 46.2 14.4 214.0 4650.0 NaN
324 Gentoo Biscoe 47.3 13.8 216.0 4725.0 NaN
336 Gentoo Biscoe 44.5 15.7 217.0 4875.0 NaN
339 Gentoo Biscoe NaN NaN NaN NaN NaN

It is always good practice to check your work. This can be challenging when dealing with large data sets because you can't keep printing them out and checking every item to make sure that no errors have been introduced.

One way to make sure that these commands didn't do something unexpected behind the scenes is just to plot each data set and make sure they look the same.

For example:

In [18]:
sns.scatterplot(data=dfp, x="body_mass_g", y="bill_depth_mm")
Out[18]:
<AxesSubplot:xlabel='body_mass_g', ylabel='bill_depth_mm'>
In [19]:
sns.scatterplot(data=dfp1, x="body_mass_g", y="bill_depth_mm")
Out[19]:
<AxesSubplot:xlabel='body_mass_g', ylabel='bill_depth_mm'>

Alternatively, the describe() function prints summary statistics. These should be the same for each.

Below we see how this works. What do you think? Is everything broadly OK with our data set?

Can you explain the differences?

In [20]:
dfp.describe()
Out[20]:
bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
count 342.000000 342.000000 342.000000 342.000000
mean 43.921930 17.151170 200.915205 4201.754386
std 5.459584 1.974793 14.061714 801.954536
min 32.100000 13.100000 172.000000 2700.000000
25% 39.225000 15.600000 190.000000 3550.000000
50% 44.450000 17.300000 197.000000 4050.000000
75% 48.500000 18.700000 213.000000 4750.000000
max 59.600000 21.500000 231.000000 6300.000000
In [21]:
dfp1.describe()
Out[21]:
bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
count 344.000000 344.000000 344.000000 344.000000
mean 43.921930 17.151170 200.915205 4201.754386
std 5.443643 1.969027 14.020657 799.613058
min 32.100000 13.100000 172.000000 2700.000000
25% 39.275000 15.600000 190.000000 3550.000000
50% 44.250000 17.300000 197.000000 4050.000000
75% 48.500000 18.700000 213.000000 4750.000000
max 59.600000 21.500000 231.000000 6300.000000

Data Engineering - our second method¶

In the method above we just replaced missing values with (hopefully) nearby ones.

On the other hand, if we have a lot of data and are able to live with a little less of it then we can just drop the data items (rows) that contain one or more undefined values.

THINK ABOUT: what could go wrong?

For example: let's recall the rows with NaN entries and then total up how many there are in each column, and in total:

In [22]:
dfp.loc[NaN_rows.index]
Out[22]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
3 Adelie Torgersen NaN NaN NaN NaN NaN
8 Adelie Torgersen 34.1 18.1 193.0 3475.0 NaN
9 Adelie Torgersen 42.0 20.2 190.0 4250.0 NaN
10 Adelie Torgersen 37.8 17.1 186.0 3300.0 NaN
11 Adelie Torgersen 37.8 17.3 180.0 3700.0 NaN
47 Adelie Dream 37.5 18.9 179.0 2975.0 NaN
246 Gentoo Biscoe 44.5 14.3 216.0 4100.0 NaN
286 Gentoo Biscoe 46.2 14.4 214.0 4650.0 NaN
324 Gentoo Biscoe 47.3 13.8 216.0 4725.0 NaN
336 Gentoo Biscoe 44.5 15.7 217.0 4875.0 NaN
339 Gentoo Biscoe NaN NaN NaN NaN NaN
In [23]:
dfp.isna().sum()
Out[23]:
species               0
island                0
bill_length_mm        2
bill_depth_mm         2
flipper_length_mm     2
body_mass_g           2
sex                  11
dtype: int64

We could have written dfp.isna().sum(axis=0) to insist that we are counting down columns here, but that's the default so the axis=0 isn't needed.

We can see that there are no more that two NaN values in the third to sixth columns, but eleven in the last, the seventh, column.

NOTE: the digit in the left most column is just the index of the column - it is not considered part of the data set.

So, given that we have 344 data points (penguins), it looks like we can afford to drop these bad data rows from the set. We can do it like this:

In [24]:
dfp2 = dfp.dropna()

Let's compare...

In [25]:
dfp
Out[25]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
0 Adelie Torgersen 39.1 18.7 181.0 3750.0 Male
1 Adelie Torgersen 39.5 17.4 186.0 3800.0 Female
2 Adelie Torgersen 40.3 18.0 195.0 3250.0 Female
3 Adelie Torgersen NaN NaN NaN NaN NaN
4 Adelie Torgersen 36.7 19.3 193.0 3450.0 Female
... ... ... ... ... ... ... ...
339 Gentoo Biscoe NaN NaN NaN NaN NaN
340 Gentoo Biscoe 46.8 14.3 215.0 4850.0 Female
341 Gentoo Biscoe 50.4 15.7 222.0 5750.0 Male
342 Gentoo Biscoe 45.2 14.8 212.0 5200.0 Female
343 Gentoo Biscoe 49.9 16.1 213.0 5400.0 Male

344 rows × 7 columns

In [26]:
dfp2
Out[26]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
0 Adelie Torgersen 39.1 18.7 181.0 3750.0 Male
1 Adelie Torgersen 39.5 17.4 186.0 3800.0 Female
2 Adelie Torgersen 40.3 18.0 195.0 3250.0 Female
4 Adelie Torgersen 36.7 19.3 193.0 3450.0 Female
5 Adelie Torgersen 39.3 20.6 190.0 3650.0 Male
... ... ... ... ... ... ... ...
338 Gentoo Biscoe 47.2 13.7 214.0 4925.0 Female
340 Gentoo Biscoe 46.8 14.3 215.0 4850.0 Female
341 Gentoo Biscoe 50.4 15.7 222.0 5750.0 Male
342 Gentoo Biscoe 45.2 14.8 212.0 5200.0 Female
343 Gentoo Biscoe 49.9 16.1 213.0 5400.0 Male

333 rows × 7 columns

It looks fine - the NaN values have disappeared from the newly engineered dataset. We can check, as above, by counting how many NaN's are found in the new data set:

In [27]:
dfp2.isna().sum()
Out[27]:
species              0
island               0
bill_length_mm       0
bill_depth_mm        0
flipper_length_mm    0
body_mass_g          0
sex                  0
dtype: int64

On the other hand, the index values in the left most column are off. There is no 3 for example. We can reset them with the reset_index() function but we have to make sure we drop the original indices otherwise they will persist.

In [28]:
# don't do this - you'll just a column of old and useless index labels.
# dfp2 = dfp2.reset_index()
# instead reset the index and drop the original index column
dfp2 = dfp2.reset_index(drop=True)
In [29]:
dfp2
Out[29]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
0 Adelie Torgersen 39.1 18.7 181.0 3750.0 Male
1 Adelie Torgersen 39.5 17.4 186.0 3800.0 Female
2 Adelie Torgersen 40.3 18.0 195.0 3250.0 Female
3 Adelie Torgersen 36.7 19.3 193.0 3450.0 Female
4 Adelie Torgersen 39.3 20.6 190.0 3650.0 Male
... ... ... ... ... ... ... ...
328 Gentoo Biscoe 47.2 13.7 214.0 4925.0 Female
329 Gentoo Biscoe 46.8 14.3 215.0 4850.0 Female
330 Gentoo Biscoe 50.4 15.7 222.0 5750.0 Male
331 Gentoo Biscoe 45.2 14.8 212.0 5200.0 Female
332 Gentoo Biscoe 49.9 16.1 213.0 5400.0 Male

333 rows × 7 columns

Now we have a clean data set with no false values introduced, with no undefined entries, and with consecutive labelling down the left.

Visualization¶

Data sets are often much too large to be able to effectively work with them in tabular form. Visualization is then more useful.

Let's pause to explore a few visuals of our cleaned-up data set.

In [30]:
sns.scatterplot(data=dfp2, x="bill_length_mm", y="bill_depth_mm", hue="species")
Out[30]:
<AxesSubplot:xlabel='bill_length_mm', ylabel='bill_depth_mm'>
In [31]:
sns.scatterplot(data=dfp2, x="body_mass_g", y="flipper_length_mm", hue="species")
Out[31]:
<AxesSubplot:xlabel='body_mass_g', ylabel='flipper_length_mm'>
In [32]:
sns.pairplot(dfp2, hue='species')
Out[32]:
<seaborn.axisgrid.PairGrid at 0x7f81f83c7940>
In [33]:
# lots of options for the above. See
# https://seaborn.pydata.org/generated/seaborn.pairplot.html
sns.pairplot(dfp2, corner=True, hue='species', height=1.5)
Out[33]:
<seaborn.axisgrid.PairGrid at 0x7f82194985f8>
In [34]:
g = sns.pairplot(dfp2, diag_kind="kde", hue='species')
g.map_lower(sns.kdeplot, levels=4, color=".2")
Out[34]:
<seaborn.axisgrid.PairGrid at 0x7f8248eb6470>

Further Exploration of the Data Set¶

So far we have loaded the data, and operated on it row by row as well as plotted various views of the data.

Let's look now at how to manipulate the data set at a lower level, and see how we might separate out clusters of data - data items that each share a common feature.

Recall, this is what our set contains...

In [35]:
dfp2.head()
Out[35]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
0 Adelie Torgersen 39.1 18.7 181.0 3750.0 Male
1 Adelie Torgersen 39.5 17.4 186.0 3800.0 Female
2 Adelie Torgersen 40.3 18.0 195.0 3250.0 Female
3 Adelie Torgersen 36.7 19.3 193.0 3450.0 Female
4 Adelie Torgersen 39.3 20.6 190.0 3650.0 Male

We can see how the species form almost distinct clusters with the following plot.

In [36]:
sns.scatterplot(data=dfp2, x="bill_length_mm", y="bill_depth_mm", hue="species")
Out[36]:
<AxesSubplot:xlabel='bill_length_mm', ylabel='bill_depth_mm'>

We can access the column of species data using square brackets like this

dfp2['species']

This refers to every row - with lots of repeated values. In fact they wont all get printed out.

In [37]:
dfp2['species']
Out[37]:
0      Adelie
1      Adelie
2      Adelie
3      Adelie
4      Adelie
        ...  
328    Gentoo
329    Gentoo
330    Gentoo
331    Gentoo
332    Gentoo
Name: species, Length: 333, dtype: object

We can squeeze out the repeats into just one uniquely occuring feature value like this...

In [38]:
dfp2['species'].unique()
Out[38]:
array(['Adelie', 'Chinstrap', 'Gentoo'], dtype=object)

This tells us that there are three unique species. We knew this from the plots - but that was a human taking a look. This method allows the code to determine the same information without human intervention.

Creating Data Subsets¶

It is sometimes useful to be able to separate out the data subsets, by a given feature value. If we choose to separate by 'species' then this command

dfp2.loc[ dfp2['species'] == 'Adelie' ]

will give us back a new data frame that just contains the Adelie penguin data. It does this by using square brackets and double equals so that this statement,

dfp2['species'] == 'Adelie'

evaluates to true if, for a given row, the species feature is Adelie. Then

dfp2.loc[ ? ]

keeps only those rows for which the question mark is true. We can assign these rows to a new data frame.

This means that we can create three data subsets - one for each species - as follows...

In [39]:
dfA = dfp2.loc[dfp2['species'] == 'Adelie']
dfC = dfp2.loc[dfp2['species'] == 'Chinstrap']
dfG = dfp2.loc[dfp2['species'] == 'Gentoo']

Using matplotlib to plot the clusters separately¶

We can use plt.scatter to plot scatter plots directly in matplotlib as below. First we create arrays (vectors if you like) of values, and then we plot them in 2D.

In [40]:
blA=np.array(dfA['bill_length_mm'].tolist())
bdA=np.array(dfA['bill_depth_mm'].tolist())
plt.scatter(blA,bdA,color='blue')

blC=np.array(dfC['bill_length_mm'].tolist())
bdC=np.array(dfC['bill_depth_mm'].tolist())
plt.scatter(blC,bdC,color='orange')

blG=np.array(dfG['bill_length_mm'].tolist())
bdG=np.array(dfG['bill_depth_mm'].tolist())
plt.scatter(blG,bdG,color='green')
plt.xlabel('bill_length_mm')
plt.ylabel('bill_depth_mm')
plt.legend(['Adelie', 'Chinstrap', 'Gentoo'],loc='lower right')
Out[40]:
<matplotlib.legend.Legend at 0x7f821984bc18>

Interpreting the plot. We can get some statistics by using describe - as we have seen before. By comparing the means, below, with the plot above we can check that all is as it should be.

Finding short cut ways to sanity check your working like this is useful.

Here dfA is plotted in blue, and we can check that the means look reasonable given the axis labelling.

In [41]:
dfA.describe()
Out[41]:
bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
count 146.000000 146.000000 146.000000 146.000000
mean 38.823973 18.347260 190.102740 3706.164384
std 2.662597 1.219338 6.521825 458.620135
min 32.100000 15.500000 172.000000 2850.000000
25% 36.725000 17.500000 186.000000 3362.500000
50% 38.850000 18.400000 190.000000 3700.000000
75% 40.775000 19.000000 195.000000 4000.000000
max 46.000000 21.500000 210.000000 4775.000000

If you are interested in the arrays that we created in order to do these plots you can take a look at them like this.

In [42]:
blA
Out[42]:
array([39.1, 39.5, 40.3, 36.7, 39.3, 38.9, 39.2, 41.1, 38.6, 34.6, 36.6,
       38.7, 42.5, 34.4, 46. , 37.8, 37.7, 35.9, 38.2, 38.8, 35.3, 40.6,
       40.5, 37.9, 40.5, 39.5, 37.2, 39.5, 40.9, 36.4, 39.2, 38.8, 42.2,
       37.6, 39.8, 36.5, 40.8, 36. , 44.1, 37. , 39.6, 41.1, 36. , 42.3,
       39.6, 40.1, 35. , 42. , 34.5, 41.4, 39. , 40.6, 36.5, 37.6, 35.7,
       41.3, 37.6, 41.1, 36.4, 41.6, 35.5, 41.1, 35.9, 41.8, 33.5, 39.7,
       39.6, 45.8, 35.5, 42.8, 40.9, 37.2, 36.2, 42.1, 34.6, 42.9, 36.7,
       35.1, 37.3, 41.3, 36.3, 36.9, 38.3, 38.9, 35.7, 41.1, 34. , 39.6,
       36.2, 40.8, 38.1, 40.3, 33.1, 43.2, 35. , 41. , 37.7, 37.8, 37.9,
       39.7, 38.6, 38.2, 38.1, 43.2, 38.1, 45.6, 39.7, 42.2, 39.6, 42.7,
       38.6, 37.3, 35.7, 41.1, 36.2, 37.7, 40.2, 41.4, 35.2, 40.6, 38.8,
       41.5, 39. , 44.1, 38.5, 43.1, 36.8, 37.5, 38.1, 41.1, 35.6, 40.2,
       37. , 39.7, 40.2, 40.6, 32.1, 40.7, 37.3, 39. , 39.2, 36.6, 36. ,
       37.8, 36. , 41.5])

These are numpy arrays. There are a number of ways that you can select out just a subset of an array by using square brackets with slicing.

For example, we can look at the third to fifth entries like this:

blA[2:5]

Indexing starts at zero, hence the 2. The 5 denotes the first index that is not used. This is confusing so watch out for it.

In [43]:
blA[2:5]
Out[43]:
array([40.3, 36.7, 39.3])

And we can look at all entries except the last five like this:

In [44]:
blA[:-5]
Out[44]:
array([39.1, 39.5, 40.3, 36.7, 39.3, 38.9, 39.2, 41.1, 38.6, 34.6, 36.6,
       38.7, 42.5, 34.4, 46. , 37.8, 37.7, 35.9, 38.2, 38.8, 35.3, 40.6,
       40.5, 37.9, 40.5, 39.5, 37.2, 39.5, 40.9, 36.4, 39.2, 38.8, 42.2,
       37.6, 39.8, 36.5, 40.8, 36. , 44.1, 37. , 39.6, 41.1, 36. , 42.3,
       39.6, 40.1, 35. , 42. , 34.5, 41.4, 39. , 40.6, 36.5, 37.6, 35.7,
       41.3, 37.6, 41.1, 36.4, 41.6, 35.5, 41.1, 35.9, 41.8, 33.5, 39.7,
       39.6, 45.8, 35.5, 42.8, 40.9, 37.2, 36.2, 42.1, 34.6, 42.9, 36.7,
       35.1, 37.3, 41.3, 36.3, 36.9, 38.3, 38.9, 35.7, 41.1, 34. , 39.6,
       36.2, 40.8, 38.1, 40.3, 33.1, 43.2, 35. , 41. , 37.7, 37.8, 37.9,
       39.7, 38.6, 38.2, 38.1, 43.2, 38.1, 45.6, 39.7, 42.2, 39.6, 42.7,
       38.6, 37.3, 35.7, 41.1, 36.2, 37.7, 40.2, 41.4, 35.2, 40.6, 38.8,
       41.5, 39. , 44.1, 38.5, 43.1, 36.8, 37.5, 38.1, 41.1, 35.6, 40.2,
       37. , 39.7, 40.2, 40.6, 32.1, 40.7, 37.3, 39. , 39.2])

Let's look now at how we can interrogate our three smaller data subsets.

Here are two ways to determine the number of rows in each.

First, using shape[0]...

In [45]:
print('number of rows in dfA = ', dfA.shape[0], '; in dfC = ', dfC.shape[0], ' and in dfG = ', dfG.shape[0])

number of rows in dfA =  146 ; in dfC =  68  and in dfG =  119

And second using the fact that shape provides a list of two values, and we can ignore the second with _...

In [46]:
rA, _ = dfA.shape; rC, _ = dfC.shape; rG, _ = dfG.shape
print('number of rows in dfA = ', rA, '; in dfC = ', rC, ' and in dfG = ', rG)

number of rows in dfA =  146 ; in dfC =  68  and in dfG =  119

Each of these can be used to determine how many of each species there are, because there is one row for each penguin in each data subset.

$k$-NN's - developing intuition¶

We can now look at the $k$ Nearest Neighbours, or $k$-NN, method for classification of data.

The setting we assume at the outset is that we have a 'training set' of data such that each row of the data set corresponds to one observation.

Moreover, in each row there are numerical features which can be organized into a vector, $\boldsymbol{x}=(x_1,x_2,\ldots,x_n)^T$, and a label, $y$, which is categorical.

There may be other numerical and categorical data that we choose not to use.

We imagine plotting these data points in $n$-dimensional space (hard to imagine when $n>3$, which is why the abstraction of mathematics is so useful), and we imagine them being coloured according to the value of the label $y$.

In the example above we had

\begin{align} \boldsymbol{x} & = (\mathtt{bill\underline{\ }length\underline{\ }mm}, \mathtt{bill\underline{\ }depth\underline{\ }mm})^T \\ y & = (\mathtt{Adelie}, \mathtt{Chinstrap}, \mathtt{Gentoo})^T \end{align}

and we coloured the labels as blue, orange or green.

Now imagine that a field researcher reports in some new measurements for a penguin, and that we want to classify its species based only on those measurements.

The idea is to plot the new measurements and see which cluster of like colour they are closest to. This closest cluster (colour) is then used to assign the species to that new measurement.

Let's see a dummy run of this in a picture.

In the diagram below we pretend that we only have the first twenty rows of each of the data subsets. We plot them as coloured dots, just as above.

Then we pretend that we get three new observations. For illustration purposes we take the entries from the fourth from last position in each data set.

But in the REAL WORLD we would be expecting new data to be arriving UNSEEN from the field.

We plot these 'new observations' with a cross.

In [47]:
# plot first twenty rows of each as coloured dots.
plt.scatter(blA[0:20],bdA[0:20],color='blue')
plt.scatter(blC[0:20],bdC[0:20],color='orange')
plt.scatter(blG[0:20],bdG[0:20],color='green')
plt.legend(['Adelie', 'Chinstrap', 'Gentoo'],loc='lower right')
plt.xlabel('bill_length_mm')
plt.ylabel('bill_depth_mm')

# pick out the data item fourth from the end in each
indx = -4
# and plot each as a cross
plt.scatter(blA[indx],bdA[indx],color='blue', marker='x', s=500)
plt.scatter(blC[indx],bdC[indx],color='orange', marker='x', s=500)
plt.scatter(blG[indx],bdG[indx],color='green', marker='x', s=500)
Out[47]:
<matplotlib.collections.PathCollection at 0x7f81f8698320>

We carry out the classification as follows:

  1. The green cross is quite central in the green, Gentoo, cluster and so we can classify this new observation as a Gentoo penguin.

  2. The blue cross isn't that central in the blue cluster, but on the other hand it is far away from the yellow and green clusters and so we can safely classify this observation as an Adelie penguin.

  3. The yellow cross presents us with more of a dilemma though. A careful look suggests that it is slightly closer to the yellow cluster than the blue and so, on that basis, we would probably choose to classify that penguin as a Chinstrap.

Any comments, thoughts, questions?¶

The first two steps seem safe, and justifiable. They are explainable. The third less so. We can see that the yellow cross corresponds to a fairly typical bill depth for an Adelie.

  • So is it a Chinstrap?

  • We can also see that Adelie penguins have bill lengths that straddle the value indicated by the yellow cross.

  • So should the yellow cross observation be classified as a Chinstrap?

  • We see here that the issue of explainability can be vexed.

  • If we had more data the yellow cross might become obviously a Chinstrap,

  • Or it might be obvious that it is an Adelie.

Explainability may or may not matter. But it is increasingly becoming a hot topic in data science.

Suppose your pension fund invested everything in a new tech venture that was going to design batteries with infinite life. It will fail of course.

If this venture was suggested by an Artificially Intelligent agent powered by machine learning algorithms then the pension company directors wont be able to explain their reasoning if the underlying data science was not explainable.

This is hardly realistic, but explainability is a big and important deal in areas like finance and investing, and in medical diagnosis, to name but two. The reasons for its importance are obvious.

$k$-NN's - the mathematical details¶

We index each data point in the training set with a subscript. So we have the feature vectors $\boldsymbol{x}_1$, $\boldsymbol{x}_2$, $\boldsymbol{x}_3$, $\ldots$. Each of these has a label, $y_1$, $y_2$, $y_3$, $\ldots$.

These are the coloured dots above. The positions are the features. The colours are the labels.

We now get a new observation, $\boldsymbol{x}^*$ and we want to classify it - we want to apply a label to it using the data from the training set.

The mathematical version of the process we followed above was to determine the distance between $\boldsymbol{x}^*$ and each $\boldsymbol{x}_i$ using

$$ \Vert\boldsymbol{x}^* - \boldsymbol{x}_i\Vert_2 \qquad\text{(recall: the Euclidean, Pythagorean or $\ell_2$ norm).} $$

We then to choose the value $i$ such that this distance is a minimum. The label, $y_i$, corresponding to that particular $i$ is then assigned to the new observation $\boldsymbol{x}^*$.

Cross-Reference to the Assigned Reading¶

You were recommended to read pages 19 - 25 of

  • MLFCES: Machine Learning: A First Course for Engineers and Scientists, by Andreas Lindholm, Niklas Wahlström, Fredrik Lindsten, Thomas B. Schön. Cambridge University Press. http://smlbook.org.

More details on this are given there, in paticular:

  • the use of $k$-NN for regression as well as classification.
  • the use of more than one 'nearest' neighbour - see which cluster 'wins' a vote.
  • notes on how to choose the number of neighbours, and 'overfitting'.
  • the importance of normalizing the inputs

Also of importance, but not mentioned in the book, is the choice of norm. We referred to the Euclidean or Pythagorean norm above, but we could just as easily have chosen any of the other $p$ norms that we discussed when we reviewed the material on vectors.

Hyperparameters¶

In the discussion above we just touched upon the important issue of picking hyperparameters. These are values and choices that need to be specified to the algorithm, the code, prior to the machine learning phase.

In the above we mentioned that we need to choose:

  • $k$ - the number of nearest neighbours to search for.
  • $p$ - the choice of norm to use to measure distance, nearness.

These are human choices: the hyperparameters are not learned from the data, but need to be chosen upfront.

Data Set Bifurcation and Trifurcation¶

However, we don't necessarily need to worry about making a wrong choice of hyperparameters that cannot subsequently be changed. In practice we would be prepared to calibrate the model by tuning its performance by turning the dials on the hyperparameter values.

Usually the dataset that we are working with will be either bifurcated into a training and a test set. Or will be trifurcated into a training, validation and a test set.

We'll return to this as we go through, but briefly...

  • The training set: used to initialise the machine learning model.
  • The validation set: used to tune the hyperparameters.
  • The test set: used as unseen data to derive final performance quality measurements after training and validation has been completed.

It is important to realise that the test set output should never be used to further tune and calibrate the model. It is a hold out set that simulates how the model will perform in the real world on unseen data.

The data set is treated in all of these cases as ground truth - it is believed to be true, although in practice some data points might contain errors, or be missing. And there is almost certainly going to be some noise on any numerical values recorded in the data.

There no hard and fast rules on the proportions to use to bifurcate or trifurcate the data set. We might bifurcate using 75%/25% for example, or trifurcate with 50%/25%/25%.

Introducing scikit-learn, our first visit¶

Let's now see now how to use scikit-learn to do $k$-NN classification with the penguins data that we cleaned and prepared.

The following code was adapted in its early stages from Machine Learning with Python, tutorialspoint as found here https://www.tutorialspoint.com/machine_learning_with_python/index.htm or here https://www.tutorialspoint.com/machine_learning_with_python/machine_learning_with_python_tutorial.pdf

You'll have seen a number of instances by now in these notebooks where external sources are liberally referenced. Feel free to do this - but make sure that you always acknowledge your sources.

We are going to work with the entire cleaned-up penguins data set that we originally stored in dfp2.

Let's remember what it loked like...

In [48]:
dfp2.head()
Out[48]:
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g sex
0 Adelie Torgersen 39.1 18.7 181.0 3750.0 Male
1 Adelie Torgersen 39.5 17.4 186.0 3800.0 Female
2 Adelie Torgersen 40.3 18.0 195.0 3250.0 Female
3 Adelie Torgersen 36.7 19.3 193.0 3450.0 Female
4 Adelie Torgersen 39.3 20.6 190.0 3650.0 Male

We want to use the numerical features (values) in each row to predict species.

Before we start using the sklearn python library we need to see how we can pick these data items out using array slicing.

First, we can pick out the value of the species with this command (the colon part is important - it refers to column zero)

dfp2.iloc[2, 0:1].values

This refers to the entry in the third, the '2', row and first, the '0:1', column.

To refer to all rows we replace the 2 with a colon : - as we'll see below.

Let's see it in action...

In [49]:
dfp2.iloc[2, 0:1].values
Out[49]:
array(['Adelie'], dtype=object)

Second, we can refer to the four numerical features with this command

dfp2.iloc[1, 2:6].values

which refers to second row, and columns three to six inclusive. Once again we will use a colon to refer to all rows.

Again, let's see this in action...

In [50]:
dfp2.iloc[1, 2:6].values
Out[50]:
array([39.5, 17.4, 186.0, 3800.0], dtype=object)

Using sklearn¶

We will now fit the $k$-NN model using the Manhattan, or taxicab, norm, which we also call the $p=1$ norm:

$$ \Vert\boldsymbol{x}^* - \boldsymbol{x}_i\Vert_1. $$

In addition, we will use two ($k=2$) nearest neighbours, and we will also obtain something called the confusion matrix, and will print some performance data.

The last two of these will be re-visited because they exhibit two very important means in which we can assess the performance of our model.

Typically we assign the data set features to a variable called X, and the data set labels to a variable called y. Using the array slicing that we saw above this is straightforward...

In [51]:
# We assign the numerical features to X
X = dfp2.iloc[:, 2:6].values
# And we assign the species label to y
y = dfp2.iloc[:, 0].values

We could bifurcate the data into a training and test set ourselves, but sklearn provides a helper function for this. It is called train_test_split.

First we have to import it. Then we give it X and y and specify the proportion of the data that we use for the hold out, or test set. we'll specify that 40% of the data should be reserved for testing.

In [52]:
# from the scikit-learn library we use 40% of the data to test
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.40)

The function returns four subsets of data:

X_train - 60% of the data set features to be used to configure the model
X_test  - 40% of the data set features to used to test the configured model
y_train - 60% of the data set features matching the X_train features
y_test  - 40% of the data set features matching the X_test features

We can look at the sizes of each of these by using shape as follows...

In [53]:
print('shape of X_train = ', X_train.shape,' and of X_test = ', X_test.shape)
print('shape of y_train = ', y_train.shape,' and of y_test = ', y_test.shape)

shape of X_train =  (199, 4)  and of X_test =  (134, 4)
shape of y_train =  (199,)  and of y_test =  (134,)

Normalization of Data¶

The next step is to normalize the feature data - the importance and role of this step is discussed in the recommended reading of pages 19 - 25 [MLFCES]. Again, sklearn provides a helper function for this called StandardScaler. This will remove the mean from the data and scale to unit variance. You can read more about this here: https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.StandardScaler.html

In [54]:
# import the helper and give it a name
from sklearn.preprocessing import StandardScaler
scaler = StandardScaler()
# initialise the scaler by feeding it the training data
scaler.fit(X_train)
# now carry out the transformation of all of the feauture data
X_train = scaler.transform(X_train)
X_test = scaler.transform(X_test)

REMARK: note that X_train is used to provide the scaling data, and not X_test. This is because X_test is hold out data. We must treat it as unseen. We can freely transform it though, because that can be done without actually looking at it.

Fitting: Learning from Data¶

We can now bring in the $k$-NN classifier method from sklearn and obtain a classifier object that uses $k=2$ nearest neighbours and the $p=1$ norm.

In [55]:
# import the k-NN classifier
from sklearn.neighbors import KNeighborsClassifier
# assign it with k=2 and p=1
classifier = KNeighborsClassifier(n_neighbors=2, p=1)
# give the training data to the classifier
classifier.fit(X_train, y_train)
Out[55]:
KNeighborsClassifier(n_neighbors=2, p=1)

The last step above is just like the coloured cluster plots above before we plotted the larger crosses. The model now has knowledge of these clusters, this is an example of machine learning.

By giving the model the unseen test data we are in effect telling it where the large crosses are. The model then finds the two nearest neighbours, using the manhattan norm, to classify the species of those crosses. This produces predictions of the species in y_test, and we call these predicted species values y_pred.

So, with the crosses as the features in the test set, we feed this in to the classifier and obtain the predicted values as follows...

In [56]:
y_pred = classifier.predict(X_test)

Evaluation of Performance¶

Now we come to the real crux of the matter. We know what X_test should produce as species values - they are in y_test. What we actually get though are y_pred. If y_pred = y_test then we should be very happy because it indicates that the model works very well on unseen data.

In practice though, it is unlikely that each of the 134 elements in y_pred will match every one of the corresponding values in y_test.

We have several tools available to assess the quality of the model. We'll take a quick look at a couple of these now, with a brief explanation, and we'll return many times to them later and understand them in more detail.

First we import the helper functions. Then we obtain and print the confusion matrix, next some statistics in a classification report, and then an accuracy score.

In [57]:
from sklearn.metrics import classification_report, confusion_matrix, accuracy_score
cm = confusion_matrix(y_test, y_pred)
print("Confusion Matrix:")
print(cm)

clsrep = classification_report(y_test, y_pred)
print("Classification Report:",)
print(clsrep)

accsc = accuracy_score(y_test,y_pred)
print("Accuracy:", accsc)

Confusion Matrix:
[[61  0  0]
 [ 5 25  0]
 [ 0  0 43]]
Classification Report:
              precision    recall  f1-score   support

      Adelie       0.92      1.00      0.96        61
   Chinstrap       1.00      0.83      0.91        30
      Gentoo       1.00      1.00      1.00        43

    accuracy                           0.96       134
   macro avg       0.97      0.94      0.96       134
weighted avg       0.97      0.96      0.96       134

Accuracy: 0.9626865671641791

We'll come back to the classification report later, and for now just note that the accuracy score tells us the proportion of the test set for which the species was correctly predicted.

What we want to spend some time on here is the confusion matrix.

The Confusion Matrix¶

In [58]:
print(cm)

[[61  0  0]
 [ 5 25  0]
 [ 0  0 43]]

The confusion matrix is square with the same number of rows/columns as there are values for the label. In our case there are three possible label values: Adelie, Chinstrap, and Gentoo. We can refer to these as group 1, 2 and 3.

The entry in row $i$ and column $j$ of the confusion matrix tells us how many data points in X_test that were in group $i$ were predicted by the model to be in group $j$.

Now, the representation of the confusion matrix above is a numpy array and although it is useful for coding, it isn't very user friendly. The following code gives us something much nicer, and it is much easier to understand.

In [59]:
from sklearn.metrics import ConfusionMatrixDisplay
cmplot = ConfusionMatrixDisplay(cm, display_labels=classifier.classes_)
cmplot.plot()
plt.show()

We can now immediately get a feeling for how good the model is. The diagonal elements tell us how many species predictions match the true value. The off-diagonals tell us how many misses there are, and how they missed.

For example, the number in the middle of the top row tells us how many Adelie penguins were mistakenly predicted to be Chinstraps.

Also, the overall accuracy percentage can be determined by adding all the numbers in the matrix, calling the total $B$, and adding all the diagonal elements together, as $A$. The value of $A/B$ then tells us the proportion of correct predictions - and that is the Accuracy score above.

We haven't yet properly reviewed the mathematical concept and notion of a matrix yet, although we will do soon. We will be coming back to confusion matrices over and over again though.

Before moving on to some exercises we close with a comment about using the $k$-NN model for regression.

$k$-NN for regression¶

Above we saw how we can use $k$-N for classification: here, given feature data from an observation, we predict the label as the category the observation should be assigned to.

Regression is where the features and the labels vary in continuous sets of values. For example, we might want to predict the amount of rainfall given the number of hours of cloud, sun, daylight, along with air tempertaure, humidity and pressure.

These are all continuous variables, not discrete categorical ones.

The $k$-NN technique can also be used for regression by, in effect, turning the continuous variables into discrete ones. To get an idea of this imagine learning a function $y=f(x)$ as follows.

  • take a set of values (features) $x_1, x_2, x_3, \ldots$
  • take the corresponding labels $f(x_1), f(x_2), f(x_3), \ldots$
  • plot these points - treat each as a cluster, as above.

The predict the function value given a new point, $x^*$, we would:

  1. determine $i$ such that $\vert x^* - x_i\vert$ is minimal over all of $x_1, x_2, x_3, \ldots$.
  2. say that $x_i$ is the nearest neighbour to $x^*$
  3. estimate $f(x^*)$ by $f(x_i)$.

This will work well if $f$ is quite well-behaved: continuous and not very rapidly varying, for example.

We wont touch more on this - it isn't on our journey. If you are interested in seeing more about this though you can, for example, look here https://stackabuse.com/k-nearest-neighbors-algorithm-in-python-and-scikit-learn/ for a demonstration of this using the California house data set.

Exercise¶

Experiment with the $k$-NN classifier we just developed. For example,

  • Change the 60%/40% bifurcation
  • Change the value of $k$: decrease it to $1$, or increase it to $3,4,5,\ldots$
  • Change the norm from $p=1$ to $p>1$.
  • Does $p<1$ make any sense here?

Exercise¶

Look at the following scatter plots. Suppose we wished to predict gender from two features.

  • What two features would work best do you think?
  • Which pairs of features are unlikely to work well?
In [60]:
sns.scatterplot(data=dfp2, x="bill_length_mm", y="bill_depth_mm", style="species", hue="sex")
Out[60]:
<AxesSubplot:xlabel='bill_length_mm', ylabel='bill_depth_mm'>
In [61]:
sns.scatterplot(data=dfp2, x="flipper_length_mm", y="body_mass_g", style="species", hue="sex")
Out[61]:
<AxesSubplot:xlabel='flipper_length_mm', ylabel='body_mass_g'>
In [62]:
sns.scatterplot(data=dfp2, x="body_mass_g", y="bill_depth_mm", style="species", hue="sex")
Out[62]:
<AxesSubplot:xlabel='body_mass_g', ylabel='bill_depth_mm'>
In [63]:
sns.scatterplot(data=dfp2, x="body_mass_g", y="bill_length_mm", style="species", hue="sex")
Out[63]:
<AxesSubplot:xlabel='body_mass_g', ylabel='bill_length_mm'>
In [64]:
sns.scatterplot(data=dfp2, x="bill_length_mm", y="flipper_length_mm", style="species", hue="sex")
Out[64]:
<AxesSubplot:xlabel='bill_length_mm', ylabel='flipper_length_mm'>
In [65]:
sns.scatterplot(data=dfp2, x="bill_depth_mm", y="flipper_length_mm", style="species", hue="sex")
Out[65]:
<AxesSubplot:xlabel='bill_depth_mm', ylabel='flipper_length_mm'>

Exercise¶

The confusion matrix we generated above is a numpy array. We will be looking in much more detail at these objects - both mathematically and in code - soon, but first here is a warm up. Let's recall the matrix:

In [66]:
cm
Out[66]:
array([[61,  0,  0],
       [ 5, 25,  0],
       [ 0,  0, 43]])

We can use cm[0,0] to access the value in the first row and first column.

  • What do you think cm[1,1] and cm[2,2] refer to?
  • what do you think cm[0,0]+cm[1,1]+cm[2,2] produces?

Check your answers by using

  • print(cm[1,1],cm[2,2])
  • print(cm[0,0]+cm[1,1]+cm[2,2])
In [67]:
print(cm[1,1],cm[2,2])
print(cm[0,0]+cm[1,1]+cm[2,2])

25 43
129

What do you think cm.sum() produces? Check, or discover, with

  • print(cm.sum())
In [68]:
print(cm.sum())

134

How do you think cm[0,0]+cm[1,1]+cm[2,2] and cm.sum() relate to the Accuracy score given above? Print out your answer and check.

In [69]:
print((cm[0,0]+cm[1,1]+cm[2,2])/cm.sum())

0.9626865671641791

Compare np.trace(cm) to cm[0,0]+cm[1,1]+cm[2,2] - use your findings to shorten the command above

In [70]:
print(np.trace(cm)/cm.sum())

0.9626865671641791