README.md

ML Pipeline Steps

In this project, we use a dataset containing bone marrow transplantation characteristics for pediatric patients from UCI’s Machine Learning Repository.

We will use the dataset (http://archive.ics.uci.edu/ml/machine-learning-databases/abalone/abalone.data), to build a pipeline, containing all preprocessing and data cleaning steps, and then select the best classifier to predict patient survival.

1. Preprocessing

(a). Numeric Data Cleaning

Output:

pipeline_arr == scaled_tx_arr : True

|pipeline_arr_med - scaled_tx_arr_med| = 43.36075966952346

(b). Categorical Data Cleaning

Output:

pipeline_arr == scaled_tx_arr : True

(c). Column Transformer -> numerical & categorical

Preprocess transformer to training data:

ColumnTransformer(transformers=[('num_preprocess', Pipeline(steps=[('imputer', SimpleImputer()), ('scale', StandardScaler())]), Index(['length', 'diam', 'height', 'whole', 'shucked', 'viscera', 'shell'], dtype='object')), ('cat_preprocess', Pipeline(steps=[('imputer', SimpleImputer(strategy='most_frequent')), ('ohe', OneHotEncoder(drop='first', sparse=False))]), Index(['sex'], dtype='object'))])

Store transformed test data:

[[ 0.20638521 0.15779273 0.35112392 ... 0.68293021 0. 1.] [-0.21953343 -0.10120617 -0.47557388 ... -0.34880017 1. 0.] [ 0.8026713 0.72759029 0.35112392 ... 0.55533104 0. 1.] ...[-0.2621253 -0.10120617 -0.47557388 ... -0.37432 0. 1.] [ 0.97303876 1.03838897 0.70542298 ... 1.22249238 0. 1.] [ 0.67489571 0.67579052 0.58732329 ... 0.84334058 0. 0.]]

2. Adding Linear Regression Model

Output: $R^2$ score

pipeline score: 0.4879020616816332

sklearn metric: 0.4879020616816332

3. Hyperparameter Tuning GridSearchCV:

Output: best_score_, best_params_

GridSearchCV best score: -5.409647741106873

GridSearchCV best params: {'regr__fit_intercept': True}

4. Final Pipeline:

Output: best_regression_model, hyperparameters_of_regression_model, hyperparameters_of_imputer

The best_regression_model is: Ridge(alpha=1)

The hyperparameters_of_regression_model are: {'alpha': 1, 'copy_X': True, 'fit_intercept': True, 'max_iter': None, 'normalize': False, 'random_state': None, 'solver': 'auto', 'tol': 0.001}

The hyperparameters_of_imputer are: {'add_indicator': False, 'copy': True, 'fill_value': None, 'missing_values': nan, 'strategy': 'most_frequent', 'verbose': 0}

5. Custom Imputer:

Check custom imputer (replace missing value with mean) with 'fillna(mean):

Output:

"check both arrays are equal": True

Build ML Pipeline using UCI Bone Marrow Dataset:

-donor_age - Age of the donor at the time of hematopoietic stem cells apheresis,

-donor_age_below_35 - Is donor age less than 35 (yes, no),

-donor_ABO - ABO blood group of the donor of hematopoietic stem cells (0, A, B, AB),

-donor_CMV - Presence of cytomegalovirus infection in the donor of hematopoietic stem cells prior to transplantation (present, absent),

-recipient_age - Age of the recipient of hematopoietic stem cells at the time of transplantation,

-recipient_age_below_10 - Is recipient age below 10 (yes, no),

-recipient_age_int - Age of the recipient discretized to intervals (0,5], (5, 10], (10, 20]),

-recipient_gender - Gender of the recipient (female, male),

-recipient_body_mass - Body mass of the recipient of hematopoietic stem cells at the time of the transplantation, … -survival_status - Survival status (0 - alive, 1 - dead),

Output:

Pipeline Accuracy Test Set: 0.7894736842105263

The best classification model is: LogisticRegression()

The hyperparameters of the best classification model are: {'C': 1.0, 'class_weight': None, 'dual': False, 'fit_intercept': True, 'intercept_scaling': 1, 'l1_ratio': None, 'max_iter': 100, 'multi_class': 'auto', 'n_jobs': None, 'penalty': 'l2', 'random_state': None, 'solver': 'lbfgs', 'tol': 0.0001, 'verbose': 0, 'warm_start': False}

The number of components selected in the PCA step are: 37

Best Model Accuracy Test Set: 0.8157894736842105

Feature Engineering

1. Baseline Scoring

Dataset: https://www.kaggle.com/datasets/ryanholbrook/fe-course-data?select=concrete.csv

MAE Baseline Score: 8.232 | MAE Score with Ratio Features: 7.948

2. Mutual Information (MI)

Dataset: https://www.kaggle.com/datasets/ryanholbrook/fe-course-data?select=autos.csv

In the figure on the right, feature fuel_type has a low MI score, but it separates two price populations with different trends within the horsepower feature. This infers that fuel_type (low MI score) contributes to an interaction effect.

Dataset: https://www.kaggle.com/datasets/ryanholbrook/fe-course-data?select=ames.csv

We investigated trend lines from one category to the next to identify any interaction effect.