I have a set of data (200 rows) related to vanilla pound cake baking with 27 features, as below. The label caketaste is a measure how good the baked cake was, defined by bad(0), neutral(1), good(2).
Features = cake_id, flour_g, butter_g, sugar_g, salt_g, eggs_count, bakingpowder_g, milk_ml, water_ml, vanillaextract_ml, lemonzest_g, mixingtime_min, bakingtime_min, preheattime_min, coolingtime_min, bakingtemp_c, preheattemp_c, color_red, color_green, color_blue, traysize_small, traysize_medium, traysize_large, milktype_lowfat, milktype_skim, milktype_whole, trayshape.
Label = caketaste ["bad", "neutral", "good"]
My task is to find:
a) the 5 most important features that affects the label's outcome;
b) to find the values of the identified 5 most important features that contributed to "good" classification in the label.
I am able to solve this using sklearn (Python), fitting the data with RandomForestClassifier(), then identify the 5 most important features using Feature_Importance() which is mixingtime_min, bakingtime_min, sugar_g, flour_g and preheattemp_c.
Minimal, Complete, and Verifiable Example:
#################################################################
# a) Libraries
#################################################################
import pandas as pd
pd.plotting.register_matplotlib_converters()
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from sklearn.ensemble import RandomForestClassifier
from sklearn.impute import SimpleImputer
from sklearn.inspection import permutation_importance
from sklearn.compose import ColumnTransformer
from sklearn.model_selection import train_test_split
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import OneHotEncoder
from sklearn.preprocessing import MaxAbsScaler
from sklearn.model_selection import GridSearchCV
from sklearn.metrics import accuracy_score
import time
#################################################################
# b) Data Loading Symlinks
#################################################################
df = pd.read_excel("poundcake.xlsx", sheet_name="Sheet0", engine='openpyxl')
#################################################################
# c) Analyzing Dataframe
#################################################################
#Getting dataframe details e.g columns, total entries, data types etc
print("\n<syntax>: df.info()")
df.info()
#Getting the 1st 5 lines in the dataframe
print("\n<syntax>: df.head()")
df.head()
#################################################################
# d) Data Visualization
#################################################################
#Scatterplot SiteID vs LTE - Spectral Efficiency
fig=plt.figure()
ax=fig.add_axes([0,0,1,1])
ax.scatter(df["cake_id"], df["caketaste"], color='r')
ax.set_xlabel('cake_id')
ax.set_ylabel('caketaste')
ax.set_title('scatter plot')
plt.show()
#################################################################
# e) Feature selection
#################################################################
#Note:
#Machine learning models cannot work well with categorical (string) data, specifically scikit-learn.
#Need to convert the categorical variables into numeric types before building a machine learning model.
categorical_columns = ["trayshape"]
numerical_columns = ["flour_g","butter_g","sugar_g","salt_g","eggs_count","bakingpowder_g","milk_ml","water_ml","vanillaextract_ml","lemonzest_g","mixingtime_min","bakingtime_min","preheattime_min","coolingtime_min","bakingtemp_c","preheattemp_c","color_red","color_green","color_blue","traysize_small","traysize_medium","traysize_large","milktype_lowfat","milktype_skim","milktype_whole"]
#################################################################
# f) Dataset (Train Test Split)
#
# (Dataset)
# ┌──────────────────────────────────────────┐
# ┌──────────────────────────┬────────────┐
# | Training │ Test │
# └──────────────────────────┴────────────┘
#################################################################
# Prediction target - Training data
X = df[categorical_columns + numerical_columns]
# Prediction target - Training data
y = df["caketaste"]
# Break off validation set from training data. Default: train_size=0.75, test_size=0.25
X_train, X_test, y_train, y_test = train_test_split(X, y, train_size=0.8, test_size=0.2, random_state=42)
#################################################################
# Pipeline
#################################################################
#######################
# g) Column Transformer
#######################
categorical_encoder = OneHotEncoder(handle_unknown='ignore')
#Mean might not be suitable, Remove rows?
numerical_pipe = Pipeline([
('imp', SimpleImputer(strategy='mean'))
])
preprocessing = ColumnTransformer(
[('cat', categorical_encoder, categorical_columns),
('num', numerical_pipe, numerical_columns)])
#####################
# b) Pipeline Printer
#####################
#RF: builds multiple decision trees and merges (bagging) them together
#to get a more accurate and stable prediction (averaging).
pipe_xxx_xxx_rfo = Pipeline([
('pre', preprocessing),
('scl', None),
('pca', None),
('clf', RandomForestClassifier(random_state=42))
])
pipe_abs_xxx_rfo = Pipeline([
('pre', preprocessing),
('scl', MaxAbsScaler()),
('pca', None),
('clf', RandomForestClassifier(random_state=42))
])
#################################################################
# h) Hyper-Parameter Tuning
#################################################################
parameters_rfo = {
'clf__n_estimators':[100],
'clf__criterion':['gini'],
'clf__min_samples_split':[2,5],
'clf__min_samples_leaf':[1,2]
}
parameters_rfo_bk = {
'clf__n_estimators':[10,20,30,40,50,60,70,80,90,100,1000],
'clf__criterion':['gini','entropy'],
'clf__min_samples_split':[5,10,15,20,25,30],
'clf__min_samples_leaf':[1,2,3,4,5]
}
#########################
# i) GridSearch Printer
#########################
# scoring can be used as 'accuracy' or for MAE use 'neg_mean_absolute_error'
scr='accuracy'
grid_xxx_xxx_rfo = GridSearchCV(pipe_xxx_xxx_rfo,
param_grid=parameters_rfo,
scoring=scr,
cv=5,
refit=True)
grid_abs_xxx_rfo = GridSearchCV(pipe_abs_xxx_rfo,
param_grid=parameters_rfo,
scoring=scr,
cv=5,
refit=True)
print("Pipeline setup.... Complete")
###################################################
# Machine Learning Models Evaluation Algorithm
###################################################
grids = [grid_xxx_xxx_rfo, grid_abs_xxx_rfo]
grid_dict = { 0: 'RandomForestClassifier',
1: 'RandomForestClassifier with AbsMaxScaler',
}
# Fit the grid search objects
print('Performing model optimizations...\n')
best_test_scr = -999999999999999 #Python3 does not allow to use None anymore
best_clf = 0
best_gs = ''
for idx, grid in enumerate(grids):
start_time = time.time()
print('*' * 100)
print('\nEstimator: %s' % grid_dict[idx])
# Fit grid search
grid.fit(X_train, y_train)
#Calculate the score once and use when needed
test_scr = grid.score(X_test,y_test)
train_scr = grid.score(X_train,y_train)
# Track best (lowest grid.score) model
if test_scr > best_test_scr:
best_test_scr = test_scr
best_train_scr = train_scr
best_rf = grid
best_clf = idx
print("..........................this model is better. SELECTED")
print("Best params : %s" % grid.best_params_)
print("Training accuracy : %s" % best_train_scr)
print("Test accuracy : %s" % best_test_scr)
print("Modeling time : %s" % time.strftime("%H:%M:%S", time.gmtime(time.time() - start_time)))
print('\nClassifier with best test set score: %s' % grid_dict[best_clf])
#########################################################################################
# j) Feature Importance using Gini Importance or Mean Decrease in Impurity (MDI)
# Note:
# 1.Calculates each feature importance as the sum over the number of splits (accross
# all trees) that include the feature, proportionaly to the number of samples it splits.
# 2. Biased towards cardinality i.e numerical variables
########################################################################################
ohe = (best_rf.best_estimator_.named_steps['pre'].named_transformers_['cat'])
feature_names = ohe.get_feature_names(input_features=categorical_columns)
feature_names = np.r_[feature_names, numerical_columns]
tree_feature_importances = (best_rf.best_estimator_.named_steps['clf'].feature_importances_)
sorted_idx = tree_feature_importances.argsort()
# Figure: Top Features
count=-28
y_ticks = np.arange(0, abs(count))
fig, ax = plt.subplots()
ax.barh(y_ticks[count:], tree_feature_importances[sorted_idx][count:])
ax.set_yticklabels(feature_names[sorted_idx][count:], fontsize=7)
ax.set_yticks(y_ticks[count:])
ax.set_title("Random Forest Tree's Feature Importance from Mean Decrease in Impurity (MDI)")
fig.tight_layout()
plt.show()
What approach one can use to solve task b)? I am trying to answer the below research question,
What are the value for mixingtime_min, bakingtime_min, flour_g, sugar_g and preheattemp_c that statistically contributed for a good caketaste (Good:2) ?
Possible Expected Result:
mixingtime_min = [5,10,15] AND
bakingtime_min = [50,51,52,53,54,55] AND
flour_g = [150,160,170,180] AND
sugar_g = [200, 250] AND
preheattemp_c = [150,160,170]
The above result basically concludes if a person like to have a GOOD tasting cake, he need to bake his cake using 150-180g flour with 200-250g sugar and mixes the dough between 5-15mins, before baking it for another 50-55 mins in a preheated oven at 150-170ºC.
Hope you can give some pointers.
Question
Would you be able to guide me on how to go about approaching this research question?
Is there any library in sklearn or otherwise that able to get this information?
Any additional information such as confidence interval, outliers etc. is a bonus.
The data (poundcake.xlsx):
cake_id flour_g butter_g sugar_g salt_g eggs_count bakingpowder_g milk_ml water_ml vanillaextract_ml lemonzest_g mixingtime_min bakingtime_min preheattime_min coolingtime_min bakingtemp_c preheattemp_c color_red color_green color_blue traysize_small traysize_medium traysize_large milktype_lowfat milktype_skim milktype_whole trayshape caketaste
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from Mapping - Feature Importance vs Label classification
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