Visualizing scikit-learn pipelines in Jupyter

Visualizing scikit-learn pipelines in Jupyter#

The goal of keeping this notebook is to:

  • make it available for users that want to reproduce it locally

  • archive the script in the event we want to rerecord this video with an update in the UI of scikit-learn in a future release.

First we load the dataset#

We need to define our data and target. In this case we build a classification model

import pandas as pd

ames_housing = pd.read_csv("../datasets/house_prices.csv", na_values="?")

target_name = "SalePrice"
data, target = (
    ames_housing.drop(columns=target_name),
    ames_housing[target_name],
)
target = (target > 200_000).astype(int)

We inspect the first rows of the dataframe

data
Id MSSubClass MSZoning LotFrontage LotArea Street Alley LotShape LandContour Utilities ... ScreenPorch PoolArea PoolQC Fence MiscFeature MiscVal MoSold YrSold SaleType SaleCondition
0 1 60 RL 65.0 8450 Pave NaN Reg Lvl AllPub ... 0 0 NaN NaN NaN 0 2 2008 WD Normal
1 2 20 RL 80.0 9600 Pave NaN Reg Lvl AllPub ... 0 0 NaN NaN NaN 0 5 2007 WD Normal
2 3 60 RL 68.0 11250 Pave NaN IR1 Lvl AllPub ... 0 0 NaN NaN NaN 0 9 2008 WD Normal
3 4 70 RL 60.0 9550 Pave NaN IR1 Lvl AllPub ... 0 0 NaN NaN NaN 0 2 2006 WD Abnorml
4 5 60 RL 84.0 14260 Pave NaN IR1 Lvl AllPub ... 0 0 NaN NaN NaN 0 12 2008 WD Normal
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
1455 1456 60 RL 62.0 7917 Pave NaN Reg Lvl AllPub ... 0 0 NaN NaN NaN 0 8 2007 WD Normal
1456 1457 20 RL 85.0 13175 Pave NaN Reg Lvl AllPub ... 0 0 NaN MnPrv NaN 0 2 2010 WD Normal
1457 1458 70 RL 66.0 9042 Pave NaN Reg Lvl AllPub ... 0 0 NaN GdPrv Shed 2500 5 2010 WD Normal
1458 1459 20 RL 68.0 9717 Pave NaN Reg Lvl AllPub ... 0 0 NaN NaN NaN 0 4 2010 WD Normal
1459 1460 20 RL 75.0 9937 Pave NaN Reg Lvl AllPub ... 0 0 NaN NaN NaN 0 6 2008 WD Normal

1460 rows × 80 columns

For the sake of simplicity, we can cherry-pick some features and only retain this arbitrary subset of data:

numeric_features = ["LotArea", "FullBath", "HalfBath"]
categorical_features = ["Neighborhood", "HouseStyle"]
data = data[numeric_features + categorical_features]

Then we create the pipeline#

The first step is to define the preprocessing steps

from sklearn.pipeline import Pipeline
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import StandardScaler, OneHotEncoder

numeric_transformer = Pipeline(
    steps=[
        ("imputer", SimpleImputer(strategy="median")),
        (
            "scaler",
            StandardScaler(),
        ),
    ]
)

categorical_transformer = OneHotEncoder(handle_unknown="ignore")

The next step is to apply the transformations using ColumnTransformer

from sklearn.compose import ColumnTransformer

preprocessor = ColumnTransformer(
    transformers=[
        ("num", numeric_transformer, numeric_features),
        ("cat", categorical_transformer, categorical_features),
    ]
)

Then we define the model and join the steps in order

from sklearn.linear_model import LogisticRegression

model = Pipeline(
    steps=[
        ("preprocessor", preprocessor),
        ("classifier", LogisticRegression()),
    ]
)

Let’s visualize it!

model

Pipeline(steps=[('preprocessor',
                 ColumnTransformer(transformers=[('num',
                                                  Pipeline(steps=[('imputer',
                                                                   SimpleImputer(strategy='median')),
                                                                  ('scaler',
                                                                   StandardScaler())]),
                                                  ['LotArea', 'FullBath',
                                                   'HalfBath']),
                                                 ('cat',
                                                  OneHotEncoder(handle_unknown='ignore'),
                                                  ['Neighborhood',
                                                   'HouseStyle'])])),
                ('classifier', LogisticRegression())])
In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook.
On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.

Finally we score the model#

from sklearn.model_selection import cross_validate

cv_results = cross_validate(model, data, target, cv=5)
scores = cv_results["test_score"]
print(
    "The mean cross-validation accuracy is: "
    f"{scores.mean():.3f} ± {scores.std():.3f}"
)

The mean cross-validation accuracy is: 0.859 ± 0.018

Note

In this case, around 86% of the times the pipeline correctly predicts whether the price of a house is above or below the 200_000 dollars threshold. But be aware that this score was obtained by picking some features by hand, which is not necessarily the best thing we can do for this classification task. In this example we can hope that fitting a complex machine learning pipelines on a richer set of features can improve upon this performance level.

Reducing a price estimation problem to a binary classification problem with a single threshold at 200_000 dollars is probably too coarse to be useful in in practice. Treating this problem as a regression problem is probably a better idea. We will see later in this MOOC how to train and evaluate the performance of various regression models.

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