| name | moai-domain-data-science |
| version | 4.0.0 |
| status | production |
| description | Production-grade data science specialist with TensorFlow 2.20.0, PyTorch 2.9.0,
Scikit-learn 1.7.2 expertise. Master data processing, ML pipeline development,
model deployment, and statistical analysis. Build end-to-end data science
solutions with comprehensive experimentation and visualization.
|
| allowed-tools | ["Read","Write","Edit","Bash","Glob","WebFetch","WebSearch"] |
| tags | ["data-science","tensorflow","pytorch","scikit-learn","pandas","numpy","visualization","statistics"] |
Data Science & Analytics
Level 1: Quick Reference
Core Capabilities
- Data Processing: Pandas 2.2.0, NumPy 1.26.0, Dask 2024.1.0
- Machine Learning: TensorFlow 2.20.0, PyTorch 2.9.0, Scikit-learn 1.7.2
- Visualization: Matplotlib 3.8.0, Seaborn 0.13.0, Plotly 5.17.0
- Statistics: SciPy 1.12.0, Statsmodels 0.14.0, Pingouin 0.8.0
- Big Data: Spark 3.5.0, Polars 0.20.0, Apache Arrow 14.0.0
- Experimentation: MLflow 2.9.0, Weights & Biases, Neptune
Quick Setup Examples
# Data science workflow starter
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestClassifier
from sklearn.metrics import classification_report, confusion_matrix
# Load and explore data
df = pd.read_csv('data.csv')
print(f"Dataset shape: {df.shape}")
print(f"Missing values: {df.isnull().sum().sum()}")
# Basic preprocessing
X = df.drop('target', axis=1)
y = df['target']
# Split data
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)
# Train model
model = RandomForestClassifier(n_estimators=100, random_state=42)
model.fit(X_train, y_train)
# Evaluate
y_pred = model.predict(X_test)
print(classification_report(y_test, y_pred))
# Modern data visualization with Plotly
import plotly.express as px
import plotly.graph_objects as go
from plotly.subplots import make_subplots
# Interactive scatter plot
fig = px.scatter(df, x='feature1', y='feature2', color='target',
size='feature3', hover_data=['feature4'])
fig.show()
# Multi-subplot dashboard
fig = make_subplots(
rows=2, cols=2,
subplot_titles=('Distribution', 'Correlation', 'Time Series', 'Feature Importance')
)
# Add traces...
fig.show()
Level 2: Practical Implementation
Data Processing & Analysis Pipeline
1. Advanced Data Preprocessing
import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler, LabelEncoder, RobustScaler
from sklearn.impute import SimpleImputer, KNNImputer
from sklearn.feature_selection import SelectKBest, f_classif, RFE
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from scipy import stats
import warnings
warnings.filterwarnings('ignore')
class DataPreprocessor:
def __init__(self):
self.numeric_features = []
self.categorical_features = []
self.preprocessor = None
self.feature_selector = None
self.outlier_detector = None
def analyze_data(self, df: pd.DataFrame) -> dict:
"""Comprehensive data analysis"""
analysis = {
'shape': df.shape,
'dtypes': df.dtypes.to_dict(),
'missing_values': df.isnull().sum().to_dict(),
'missing_percentage': (df.isnull().sum() / len(df) * 100).to_dict(),
'duplicates': df.duplicated().sum(),
'numeric_summary': df.describe().to_dict(),
'categorical_summary': {},
'correlation_matrix': None
}
# Categorical features analysis
for col in df.select_dtypes(include=['object', 'category']).columns:
analysis['categorical_summary'][col] = {
'unique_count': df[col].nunique(),
'unique_values': df[col].unique().tolist()[:10], # First 10 values
'value_counts': df[col].value_counts().head().to_dict()
}
# Correlation matrix for numeric features
numeric_df = df.select_dtypes(include=[np.number])
if len(numeric_df.columns) > 1:
analysis['correlation_matrix'] = numeric_df.corr().to_dict()
return analysis
def detect_outliers(self, df: pd.DataFrame, method: str = 'iqr') -> pd.DataFrame:
"""Detect outliers using various methods"""
numeric_df = df.select_dtypes(include=[np.number])
outliers_info = {}
for col in numeric_df.columns:
if method == 'iqr':
Q1 = df[col].quantile(0.25)
Q3 = df[col].quantile(0.75)
IQR = Q3 - Q1
lower_bound = Q1 - 1.5 * IQR
upper_bound = Q3 + 1.5 * IQR
outliers = df[(df[col] < lower_bound) | (df[col] > upper_bound)]
elif method == 'zscore':
z_scores = np.abs(stats.zscore(df[col].dropna()))
outliers = df[z_scores > 3]
elif method == 'isolation_forest':
from sklearn.ensemble import IsolationForest
iso_forest = IsolationForest(contamination=0.1, random_state=42)
outlier_labels = iso_forest.fit_predict(df[[col]].dropna())
outliers = df[outlier_labels == -1]
outliers_info[col] = {
'count': len(outliers),
'percentage': len(outliers) / len(df) * 100,
'indices': outliers.index.tolist()
}
return outliers_info
def build_preprocessing_pipeline(self, X: pd.DataFrame,
handle_outliers: bool = True,
feature_selection: bool = True,
selection_method: str = 'k_best') -> Pipeline:
"""Build comprehensive preprocessing pipeline"""
# Identify feature types
self.numeric_features = X.select_dtypes(include=[np.number]).columns.tolist()
self.categorical_features = X.select_dtypes(include=['object', 'category']).columns.tolist()
# Numeric preprocessing
numeric_transformer = Pipeline(steps=[
('imputer', SimpleImputer(strategy='median')),
('scaler', RobustScaler()) # More robust to outliers than StandardScaler
])
# Categorical preprocessing
categorical_transformer = Pipeline(steps=[
('imputer', SimpleImputer(strategy='most_frequent')),
('encoder', LabelEncoder()) if len(self.categorical_features) == 1 else
('onehot', SimpleImputer(strategy='most_frequent'))
])
# Column transformer
preprocessor = ColumnTransformer(
transformers=[
('num', numeric_transformer, self.numeric_features),
('cat', categorical_transformer, self.categorical_features)
])
pipeline_steps = [('preprocessor', preprocessor)]
# Feature selection
if feature_selection and selection_method == 'k_best':
selector = SelectKBest(score_func=f_classif, k=10)
pipeline_steps.append(('feature_selection', selector))
elif feature_selection and selection_method == 'rfe':
from sklearn.ensemble import RandomForestClassifier
estimator = RandomForestClassifier(n_estimators=100, random_state=42)
selector = RFE(estimator=estimator, n_features_to_select=10)
pipeline_steps.append(('feature_selection', selector))
self.preprocessor = Pipeline(pipeline_steps)
return self.preprocessor
def transform_data(self, X: pd.DataFrame, y: pd.Series = None) -> np.ndarray:
"""Transform data using preprocessing pipeline"""
if self.preprocessor is None:
self.build_preprocessing_pipeline(X)
if y is not None:
return self.preprocessor.fit_transform(X, y)
else:
return self.preprocessor.transform(X)
def get_feature_importance(self, X: pd.DataFrame, y: pd.Series) -> dict:
"""Get feature importance using various methods"""
# Prepare data
X_processed = self.transform_data(X, y)
feature_importance = {}
# Random Forest importance
rf = RandomForestClassifier(n_estimators=100, random_state=42)
rf.fit(X_processed, y)
# Get feature names (simplified for this example)
feature_names = [f"feature_{i}" for i in range(X_processed.shape[1])]
feature_importance['random_forest'] = dict(zip(feature_names, rf.feature_importances_))
# Mutual information
from sklearn.feature_selection import mutual_info_classif
mi_scores = mutual_info_classif(X_processed, y)
feature_importance['mutual_info'] = dict(zip(feature_names, mi_scores))
# ANOVA F-test
from sklearn.feature_selection import f_classif
f_scores, _ = f_classif(X_processed, y)
feature_importance['anova_f'] = dict(zip(feature_names, f_scores))
return feature_importance
def create_features(self, df: pd.DataFrame) -> pd.DataFrame:
"""Create engineered features"""
df_engineered = df.copy()
numeric_cols = df.select_dtypes(include=[np.number]).columns
# Polynomial features for top correlated columns
if len(numeric_cols) >= 2:
# Interaction features
for i, col1 in enumerate(numeric_cols[:3]): # Limit to first 3 columns
for col2 in numeric_cols[i+1:4]: # Limit interactions
df_engineered[f'{col1}_x_{col2}'] = df[col1] * df[col2]
df_engineered[f'{col1}_div_{col2}'] = df[col1] / (df[col2] + 1e-6)
# Polynomial features
for col in numeric_cols[:3]: # Limit to first 3 columns
df_engineered[f'{col}_squared'] = df[col] ** 2
df_engineered[f'{col}_cubed'] = df[col] ** 3
df_engineered[f'{col}_log'] = np.log1p(np.abs(df[col]))
df_engineered[f'{col}_sqrt'] = np.sqrt(np.abs(df[col]))
# Statistical features
if len(numeric_cols) >= 3:
df_engineered['mean_of_numeric'] = df[numeric_cols].mean(axis=1)
df_engineered['std_of_numeric'] = df[numeric_cols].std(axis=1)
df_engineered['min_of_numeric'] = df[numeric_cols].min(axis=1)
df_engineered['max_of_numeric'] = df[numeric_cols].max(axis=1)
df_engineered['sum_of_numeric'] = df[numeric_cols].sum(axis=1)
# Date/time features (if date columns exist)
date_cols = df.select_dtypes(include=['datetime64']).columns
for col in date_cols:
df_engineered[f'{col}_year'] = df[col].dt.year
df_engineered[f'{col}_month'] = df[col].dt.month
df_engineered[f'{col}_day'] = df[col].dt.day
df_engineered[f'{col}_dayofweek'] = df[col].dt.dayofweek
df_engineered[f'{col}_quarter'] = df[col].dt.quarter
return df_engineered
# Usage example
# preprocessor = DataPreprocessor()
# analysis = preprocessor.analyze_data(df)
# outliers = preprocessor.detect_outliers(df, method='iqr')
# pipeline = preprocessor.build_preprocessing_pipeline(X)
# X_processed = preprocessor.transform_data(X, y)
# feature_importance = preprocessor.get_feature_importance(X, y)
2. Statistical Analysis & Hypothesis Testing
import scipy.stats as stats
import statsmodels.api as sm
from statsmodels.stats.power import TTestPower, GofChisquarePower
from statsmodels.stats.multicomp import pairwise_tukeyhsd
import pingouin as pg
import numpy as np
import pandas as pd
class StatisticalAnalyzer:
def __init__(self):
self.results = {}
def descriptive_statistics(self, data: pd.DataFrame,
columns: list = None) -> dict:
"""Comprehensive descriptive statistics"""
if columns is None:
columns = data.select_dtypes(include=[np.number]).columns.tolist()
stats_dict = {}
for col in columns:
series = data[col].dropna()
stats_dict[col] = {
'count': len(series),
'mean': series.mean(),
'median': series.median(),
'std': series.std(),
'var': series.var(),
'min': series.min(),
'max': series.max(),
'range': series.max() - series.min(),
'q25': series.quantile(0.25),
'q75': series.quantile(0.75),
'iqr': series.quantile(0.75) - series.quantile(0.25),
'skewness': stats.skew(series),
'kurtosis': stats.kurtosis(series),
'cv': series.std() / series.mean() if series.mean() != 0 else np.nan
}
# Confidence intervals
confidence_level = 0.95
degrees_freedom = len(series) - 1
sample_mean = series.mean()
sample_std = series.std()
standard_error = sample_std / np.sqrt(len(series))
t_critical = stats.t.ppf((1 + confidence_level) / 2, degrees_freedom)
margin_error = t_critical * standard_error
stats_dict[col]['confidence_interval'] = {
'lower': sample_mean - margin_error,
'upper': sample_mean + margin_error,
'level': confidence_level
}
return stats_dict
def normality_tests(self, data: pd.Series, alpha: float = 0.05) -> dict:
"""Test for normality using multiple methods"""
data_clean = data.dropna()
# Shapiro-Wilk test (for n < 5000)
shapiro_stat, shapiro_p = stats.shapiro(data_clean[:5000])
# Kolmogorov-Smirnov test
ks_stat, ks_p = stats.kstest(data_clean, 'norm',
args=(data_clean.mean(), data_clean.std()))
# Anderson-Darling test
ad_stat, ad_critical_values, ad_significance_levels = stats.anderson(data_clean, 'norm')
# D'Agostino's K2 test
dagostino_stat, dagostino_p = stats.normaltest(data_clean)
results = {
'shapiro_wilk': {
'statistic': shapiro_stat,
'p_value': shapiro_p,
'is_normal': shapiro_p > alpha,
'alpha': alpha
},
'kolmogorov_smirnov': {
'statistic': ks_stat,
'p_value': ks_p,
'is_normal': ks_p > alpha,
'alpha': alpha
},
'anderson_darling': {
'statistic': ad_stat,
'critical_values': dict(zip(ad_significance_levels, ad_critical_values)),
'is_normal': ad_stat < ad_critical_values[2] # 5% significance
},
'dagostino_k2': {
'statistic': dagostino_stat,
'p_value': dagostino_p,
'is_normal': dagostino_p > alpha,
'alpha': alpha
}
}
return results
def hypothesis_testing(self, data1: pd.Series, data2: pd.Series = None,
test_type: str = 'auto', alpha: float = 0.05,
alternative: str = 'two-sided') -> dict:
"""Comprehensive hypothesis testing"""
if data2 is None:
# One-sample tests
if test_type == 'auto':
# Determine appropriate test based on normality
normality = self.normality_tests(data1, alpha)
# Use t-test if data appears normal, otherwise Wilcoxon
if normality['shapiro_wilk']['is_normal']:
return self._one_sample_t_test(data1, alpha, alternative)
else:
return self._one_sample_wilcoxon_test(data1, alpha, alternative)
else:
# Two-sample tests
if test_type == 'auto':
# Check normality and equal variance assumptions
normality1 = self.normality_tests(data1, alpha)
normality2 = self.normality_tests(data2, alpha)
# Levene's test for equal variances
levene_stat, levene_p = stats.levene(data1.dropna(), data2.dropna())
if (normality1['shapiro_wilk']['is_normal'] and
normality2['shapiro_wilk']['is_normal'] and
levene_p > alpha):
# Use t-test if assumptions are met
return self._two_sample_t_test(data1, data2, alpha, alternative)
else:
# Use non-parametric test
return self._mann_whitney_test(data1, data2, alpha, alternative)
return {'error': 'Invalid test configuration'}
def _one_sample_t_test(self, data: pd.Series, alpha: float, alternative: str) -> dict:
"""One-sample t-test"""
t_stat, p_value = stats.ttest_1samp(data.dropna(), 0, alternative=alternative)
degrees_freedom = len(data.dropna()) - 1
confidence_level = 1 - alpha
# Effect size (Cohen's d)
cohens_d = data.mean() / data.std()
return {
'test': 'One-sample t-test',
'statistic': t_stat,
'p_value': p_value,
'degrees_freedom': degrees_freedom,
'alpha': alpha,
'is_significant': p_value < alpha,
'alternative': alternative,
'effect_size': cohens_d,
'effect_size_interpretation': self._interpret_cohens_d(cohens_d)
}
def _one_sample_wilcoxon_test(self, data: pd.Series, alpha: float, alternative: str) -> dict:
"""One-sample Wilcoxon signed-rank test"""
wilcoxon_stat, p_value = stats.wilcoxon(data.dropna(), alternative=alternative)
return {
'test': 'One-sample Wilcoxon signed-rank test',
'statistic': wilcoxon_stat,
'p_value': p_value,
'alpha': alpha,
'is_significant': p_value < alpha,
'alternative': alternative,
'note': 'Non-parametric test - does not assume normality'
}
def _two_sample_t_test(self, data1: pd.Series, data2: pd.Series,
alpha: float, alternative: str) -> dict:
"""Two-sample t-test"""
t_stat, p_value = stats.ttest_ind(data1.dropna(), data2.dropna(), alternative=alternative)
# Effect size (Cohen's d)
n1, n2 = len(data1.dropna()), len(data2.dropna())
pooled_std = np.sqrt(((n1-1)*data1.var() + (n2-1)*data2.var()) / (n1+n2-2))
cohens_d = (data1.mean() - data2.mean()) / pooled_std
return {
'test': 'Two-sample t-test',
'statistic': t_stat,
'p_value': p_value,
'alpha': alpha,
'is_significant': p_value < alpha,
'alternative': alternative,
'effect_size': cohens_d,
'effect_size_interpretation': self._interpret_cohens_d(cohens_d),
'sample_sizes': {'sample1': n1, 'sample2': n2}
}
def _mann_whitney_test(self, data1: pd.Series, data2: pd.Series,
alpha: float, alternative: str) -> dict:
"""Mann-Whitney U test"""
u_stat, p_value = stats.mannwhitneyu(data1.dropna(), data2.dropna(),
alternative=alternative)
return {
'test': 'Mann-Whitney U test',
'statistic': u_stat,
'p_value': p_value,
'alpha': alpha,
'is_significant': p_value < alpha,
'alternative': alternative,
'note': 'Non-parametric test - does not assume normality'
}
def _interpret_cohens_d(self, d: float) -> str:
"""Interpret Cohen's d effect size"""
abs_d = abs(d)
if abs_d < 0.2:
return 'negligible'
elif abs_d < 0.5:
return 'small'
elif abs_d < 0.8:
return 'medium'
else:
return 'large'
def correlation_analysis(self, data: pd.DataFrame,
method: str = 'pearson') -> dict:
"""Comprehensive correlation analysis"""
numeric_data = data.select_dtypes(include=[np.number])
if method == 'pearson':
corr_matrix, p_values = self._pearson_correlation(numeric_data)
elif method == 'spearman':
corr_matrix, p_values = self._spearman_correlation(numeric_data)
elif method == 'kendall':
corr_matrix, p_values = self._kendall_correlation(numeric_data)
# Find significant correlations
significant_correlations = []
for i, col1 in enumerate(numeric_data.columns):
for j, col2 in enumerate(numeric_data.columns):
if i < j: # Avoid duplicates
corr_val = corr_matrix.iloc[i, j]
p_val = p_values.iloc[i, j]
if abs(corr_val) > 0.3 and p_val < 0.05: # Thresholds
significant_correlations.append({
'variable1': col1,
'variable2': col2,
'correlation': corr_val,
'p_value': p_val,
'strength': self._interpret_correlation(corr_val)
})
return {
'correlation_matrix': corr_matrix.to_dict(),
'p_value_matrix': p_values.to_dict(),
'significant_correlations': significant_correlations,
'method': method
}
def _pearson_correlation(self, data: pd.DataFrame) -> tuple:
"""Pearson correlation with p-values"""
n = len(data)
corr_matrix = data.corr(method='pearson')
# Calculate p-values
p_values = pd.DataFrame(index=data.columns, columns=data.columns)
for i, col1 in enumerate(data.columns):
for j, col2 in enumerate(data.columns):
if i <= j:
corr, p_val = stats.pearsonr(data[col1].dropna(), data[col2].dropna())
p_values.iloc[i, j] = p_val
p_values.iloc[j, i] = p_val
else:
p_values.iloc[i, j] = p_values.iloc[j, i]
return corr_matrix, p_values
def _interpret_correlation(self, r: float) -> str:
"""Interpret correlation coefficient magnitude"""
abs_r = abs(r)
if abs_r < 0.1:
return 'negligible'
elif abs_r < 0.3:
return 'weak'
elif abs_r < 0.5:
return 'moderate'
elif abs_r < 0.7:
return 'strong'
else:
return 'very strong'
def power_analysis(self, effect_size: float, alpha: float = 0.05,
power: float = 0.8, sample_size: int = None,
test_type: str = 't-test') -> dict:
"""Statistical power analysis"""
if test_type == 't-test':
power_analysis = TTestPower()
if sample_size is None:
# Calculate required sample size
required_n = power_analysis.solve_power(
effect_size=effect_size,
alpha=alpha,
power=power,
alternative='two-sided'
)
return {
'test_type': test_type,
'required_sample_size': required_n,
'effect_size': effect_size,
'alpha': alpha,
'desired_power': power
}
else:
# Calculate achieved power
achieved_power = power_analysis.power(
effect_size=effect_size,
nobs=sample_size,
alpha=alpha,
alternative='two-sided'
)
return {
'test_type': test_type,
'sample_size': sample_size,
'achieved_power': achieved_power,
'effect_size': effect_size,
'alpha': alpha
}
return {'error': 'Unsupported test type for power analysis'}
# Usage example
# analyzer = StatisticalAnalyzer()
# desc_stats = analyzer.descriptive_statistics(df)
# normality = analyzer.normality_tests(df['column'])
# hypothesis_result = analyzer.hypothesis_testing(df['group1'], df['group2'])
# corr_analysis = analyzer.correlation_analysis(df)
# power_result = analyzer.power_analysis(effect_size=0.5, sample_size=100)
3. Machine Learning Model Development
from sklearn.model_selection import train_test_split, cross_val_score, GridSearchCV
from sklearn.ensemble import RandomForestClassifier, GradientBoostingClassifier
from sklearn.linear_model import LogisticRegression
from sklearn.svm import SVC
from sklearn.metrics import classification_report, confusion_matrix, roc_auc_score
from sklearn.preprocessing import StandardScaler
import xgboost as xgb
import lightgbm as lgb
import optuna
class MLModelBuilder:
def __init__(self):
self.models = {}
self.best_model = None
self.feature_importance = {}
self.evaluation_results = {}
def prepare_data(self, X: pd.DataFrame, y: pd.Series,
test_size: float = 0.2, random_state: int = 42) -> tuple:
"""Prepare data for machine learning"""
# Handle missing values
X_clean = X.fillna(X.median(numeric_only=True))
for col in X_clean.select_dtypes(include=['object', 'category']).columns:
X_clean[col] = X_clean[col].fillna(X_clean[col].mode()[0] if not X_clean[col].mode().empty else 'unknown')
# Encode categorical variables
X_encoded = pd.get_dummies(X_clean, drop_first=True)
# Split data
X_train, X_test, y_train, y_test = train_test_split(
X_encoded, y, test_size=test_size, random_state=random_state, stratify=y
)
return X_train, X_test, y_train, y_test
def build_base_models(self, X_train, X_test, y_train, y_test) -> dict:
"""Build and evaluate multiple base models"""
models = {
'logistic_regression': LogisticRegression(max_iter=1000, random_state=42),
'random_forest': RandomForestClassifier(n_estimators=100, random_state=42),
'gradient_boosting': GradientBoostingClassifier(random_state=42),
'xgboost': xgb.XGBClassifier(random_state=42, eval_metric='logloss'),
'lightgbm': lgb.LGBMClassifier(random_state=42, verbose=-1)
}
results = {}
for name, model in models.items():
print(f"Training {name}...")
# Train model
model.fit(X_train, y_train)
# Make predictions
y_pred = model.predict(X_test)
y_pred_proba = None
if hasattr(model, 'predict_proba'):
y_pred_proba = model.predict_proba(X_test)[:, 1]
# Evaluate
accuracy = model.score(X_test, y_test)
if len(np.unique(y_test)) == 2 and y_pred_proba is not None:
roc_auc = roc_auc_score(y_test, y_pred_proba)
else:
roc_auc = None
# Cross-validation
cv_scores = cross_val_score(model, X_train, y_train, cv=5, scoring='accuracy')
results[name] = {
'model': model,
'accuracy': accuracy,
'roc_auc': roc_auc,
'cv_mean': cv_scores.mean(),
'cv_std': cv_scores.std(),
'predictions': y_pred,
'probabilities': y_pred_proba
}
# Feature importance
if hasattr(model, 'feature_importances_'):
importance_dict = dict(zip(X_train.columns, model.feature_importances_))
self.feature_importance[name] = importance_dict
self.models = results
return results
def hyperparameter_tuning(self, X_train, y_train, model_type: str = 'random_forest',
n_trials: int = 100) -> dict:
"""Hyperparameter tuning using Optuna"""
def objective(trial):
if model_type == 'random_forest':
params = {
'n_estimators': trial.suggest_int('n_estimators', 50, 300),
'max_depth': trial.suggest_int('max_depth', 3, 20),
'min_samples_split': trial.suggest_int('min_samples_split', 2, 20),
'min_samples_leaf': trial.suggest_int('min_samples_leaf', 1, 10),
'max_features': trial.suggest_categorical('max_features', ['sqrt', 'log2', None])
}
model = RandomForestClassifier(**params, random_state=42, n_jobs=-1)
elif model_type == 'xgboost':
params = {
'n_estimators': trial.suggest_int('n_estimators', 50, 300),
'max_depth': trial.suggest_int('max_depth', 3, 10),
'learning_rate': trial.suggest_float('learning_rate', 0.01, 0.3),
'subsample': trial.suggest_float('subsample', 0.6, 1.0),
'colsample_bytree': trial.suggest_float('colsample_bytree', 0.6, 1.0),
'gamma': trial.suggest_float('gamma', 0, 5),
'reg_alpha': trial.suggest_float('reg_alpha', 0, 5),
'reg_lambda': trial.suggest_float('reg_lambda', 0, 5)
}
model = xgb.XGBClassifier(**params, random_state=42, eval_metric='logloss')
elif model_type == 'lightgbm':
params = {
'n_estimators': trial.suggest_int('n_estimators', 50, 300),
'max_depth': trial.suggest_int('max_depth', 3, 15),
'learning_rate': trial.suggest_float('learning_rate', 0.01, 0.3),
'num_leaves': trial.suggest_int('num_leaves', 20, 150),
'feature_fraction': trial.suggest_float('feature_fraction', 0.6, 1.0),
'bagging_fraction': trial.suggest_float('bagging_fraction', 0.6, 1.0),
'bagging_freq': trial.suggest_int('bagging_freq', 1, 10),
'min_child_samples': trial.suggest_int('min_child_samples', 5, 100)
}
model = lgb.LGBMClassifier(**params, random_state=42, verbose=-1)
# Cross-validation
scores = cross_val_score(model, X_train, y_train, cv=5, scoring='accuracy')
return scores.mean()
# Create study
study = optuna.create_study(direction='maximize')
study.optimize(objective, n_trials=n_trials)
# Train best model
best_params = study.best_params
if model_type == 'random_forest':
best_model = RandomForestClassifier(**best_params, random_state=42, n_jobs=-1)
elif model_type == 'xgboost':
best_model = xgb.XGBClassifier(**best_params, random_state=42, eval_metric='logloss')
elif model_type == 'lightgbm':
best_model = lgb.LGBMClassifier(**best_params, random_state=42, verbose=-1)
best_model.fit(X_train, y_train)
return {
'best_model': best_model,
'best_params': best_params,
'best_score': study.best_value,
'study': study
}
def evaluate_model(self, model, X_test, y_test, model_name: str = "model") -> dict:
"""Comprehensive model evaluation"""
# Make predictions
y_pred = model.predict(X_test)
y_pred_proba = None
if hasattr(model, 'predict_proba'):
y_pred_proba = model.predict_proba(X_test)
if len(np.unique(y_test)) == 2:
y_pred_proba_binary = y_pred_proba[:, 1]
else:
y_pred_proba_binary = None
# Basic metrics
accuracy = model.score(X_test, y_test)
# Classification report
class_report = classification_report(y_test, y_pred, output_dict=True)
# Confusion matrix
conf_matrix = confusion_matrix(y_test, y_pred)
# ROC AUC for binary classification
roc_auc = None
if y_pred_proba_binary is not None:
roc_auc = roc_auc_score(y_test, y_pred_proba_binary)
# Feature importance
feature_importance = None
if hasattr(model, 'feature_importances_'):
feature_importance = dict(zip(X_test.columns, model.feature_importances_))
evaluation = {
'model_name': model_name,
'accuracy': accuracy,
'classification_report': class_report,
'confusion_matrix': conf_matrix.tolist(),
'roc_auc': roc_auc,
'feature_importance': feature_importance,
'predictions': y_pred.tolist(),
'probabilities': y_pred_proba.tolist() if y_pred_proba is not None else None
}
self.evaluation_results[model_name] = evaluation
return evaluation
def ensemble_models(self, X_train, X_test, y_train, y_test,
models_to_ensemble: list = None) -> dict:
"""Create ensemble models"""
if models_to_ensemble is None:
models_to_ensemble = ['random_forest', 'xgboost', 'lightgbm']
# Select models for ensemble
ensemble_models = []
for model_name in models_to_ensemble:
if model_name in self.models:
ensemble_models.append((model_name, self.models[model_name]['model']))
if not ensemble_models:
raise ValueError("No valid models found for ensemble")
# Voting ensemble
from sklearn.ensemble import VotingClassifier
voting_ensemble = VotingClassifier(
estimators=ensemble_models,
voting='soft' if len(np.unique(y_train)) == 2 else 'hard'
)
voting_ensemble.fit(X_train, y_train)
voting_evaluation = self.evaluate_model(voting_ensemble, X_test, y_test, "voting_ensemble")
# Stacking ensemble
from sklearn.ensemble import StackingClassifier
base_estimators = [(name, model['model']) for name, model in self.models.items()
if name in models_to_ensemble]
stacking_ensemble = StackingClassifier(
estimators=base_estimators,
final_estimator=LogisticRegression(max_iter=1000, random_state=42),
cv=5
)
stacking_ensemble.fit(X_train, y_train)
stacking_evaluation = self.evaluate_model(stacking_ensemble, X_test, y_test, "stacking_ensemble")
return {
'voting_ensemble': voting_evaluation,
'stacking_ensemble': stacking_evaluation,
'voting_model': voting_ensemble,
'stacking_model': stacking_ensemble
}
def model_explainability(self, model, X_test, feature_names: list = None) -> dict:
"""Model explainability using SHAP and LIME"""
try:
import shap
import lime
import lime.lime_tabular
if feature_names is None:
feature_names = X_test.columns.tolist()
explainability_results = {}
# SHAP explanations
if hasattr(model, 'predict_proba'):
explainer = shap.TreeExplainer(model)
shap_values = explainer.shap_values(X_test)
# For binary classification, use the positive class
if isinstance(shap_values, list) and len(shap_values) == 2:
shap_values_positive = shap_values[1]
else:
shap_values_positive = shap_values
explainability_results['shap'] = {
'values': shap_values_positive.tolist(),
'base_values': explainer.expected_value.tolist() if hasattr(explainer.expected_value, '__iter__') else explainer.expected_value,
'feature_names': feature_names
}
# Feature importance from SHAP
shap_importance = np.abs(shap_values_positive).mean(0)
shap_importance_dict = dict(zip(feature_names, shap_importance))
explainability_results['shap_importance'] = shap_importance_dict
# LIME explanations
lime_explainer = lime.lime_tabular.LimeTabularExplainer(
X_test.values,
feature_names=feature_names,
mode='classification',
discretize_continuous=True
)
# Explain a few instances
lime_explanations = []
for i in range(min(5, len(X_test))):
exp = lime_explainer.explain_instance(
X_test.iloc[i].values,
model.predict_proba,
num_features=10
)
lime_explanations.append({
'instance_index': i,
'explanation': exp.as_list(),
'score': exp.score
})
explainability_results['lime'] = lime_explanations
except ImportError:
explainability_results = {'error': 'SHAP and LIME packages not installed'}
return explainability_results
# Usage example
# ml_builder = MLModelBuilder()
# X_train, X_test, y_train, y_test = ml_builder.prepare_data(X, y)
# base_models = ml_builder.build_base_models(X_train, X_test, y_train, y_test)
# tuning_result = ml_builder.hyperparameter_tuning(X_train, y_train, 'xgboost')
# evaluation = ml_builder.evaluate_model(tuning_result['best_model'], X_test, y_test, 'tuned_xgboost')
# ensemble_results = ml_builder.ensemble_models(X_train, X_test, y_train, y_test)
# explainability = ml_builder.model_explainability(tuning_result['best_model'], X_test)
Level 3: Advanced Integration
Production ML Systems
4. ML Pipeline with Experiment Tracking
import mlflow
import mlflow.sklearn
import mlflow.xgboost
import joblib
import json
from datetime import datetime
import os
class ProductionMLPipeline:
def __init__(self, experiment_name: str, tracking_uri: str = None):
self.experiment_name = experiment_name
if tracking_uri:
mlflow.set_tracking_uri(tracking_uri)
mlflow.set_experiment(experiment_name)
self.experiment_id = mlflow.get_experiment_by_name(experiment_name).experiment_id
self.pipeline_stages = []
self.run_id = None
def run_complete_pipeline(self, data_path: str, target_column: str,
model_types: list = None, save_models: bool = True) -> dict:
"""Run complete ML pipeline with experiment tracking"""
with mlflow.start_run(run_name=f"pipeline_run_{datetime.now().strftime('%Y%m%d_%H%M%S')}") as run:
self.run_id = run.info.run_id
# Log dataset information
mlflow.log_param("data_path", data_path)
mlflow.log_param("target_column", target_column)
# Stage 1: Data Loading and Exploration
print("Stage 1: Loading and exploring data...")
data = self._load_data(data_path)
data_info = self._explore_data(data)
for key, value in data_info.items():
if isinstance(value, (int, float)):
mlflow.log_metric(f"data_{key}", value)
else:
mlflow.log_param(f"data_{key}", str(value))
# Stage 2: Data Preprocessing
print("Stage 2: Preprocessing data...")
preprocessor = DataPreprocessor()
processed_data = preprocessor.create_features(data)
X = processed_data.drop(target_column, axis=1)
y = processed_data[target_column]
X_train, X_test, y_train, y_test = preprocessor.prepare_data(X, y)
mlflow.log_param("train_size", len(X_train))
mlflow.log_param("test_size", len(X_test))
mlflow.log_param("feature_count", X_train.shape[1])
# Stage 3: Model Training and Evaluation
print("Stage 3: Training and evaluating models...")
if model_types is None:
model_types = ['random_forest', 'xgboost', 'lightgbm']
ml_builder = MLModelBuilder()
model_results = ml_builder.build_base_models(X_train, X_test, y_train, y_test)
best_model_name = None
best_score = 0
best_model = None
for model_name, result in model_results.items():
if model_name in model_types:
# Log model metrics
mlflow.log_metric(f"{model_name}_accuracy", result['accuracy'])
mlflow.log_metric(f"{model_name}_cv_mean", result['cv_mean'])
if result['roc_auc'] is not None:
mlflow.log_metric(f"{model_name}_roc_auc", result['roc_auc'])
# Log model
try:
if 'xgboost' in model_name:
mlflow.xgboost.log_model(result['model'], f"{model_name}_model")
else:
mlflow.sklearn.log_model(result['model'], f"{model_name}_model")
except:
pass
# Track best model
if result['accuracy'] > best_score:
best_score = result['accuracy']
best_model_name = model_name
best_model = result['model']
# Stage 4: Hyperparameter Tuning for Best Model
print("Stage 4: Hyperparameter tuning...")
if best_model_name:
tuning_result = ml_builder.hyperparameter_tuning(
X_train, y_train,
model_type=best_model_name.replace('_tuned', ''),
n_trials=50
)
# Log best parameters
for param, value in tuning_result['best_params'].items():
mlflow.log_param(f"best_{param}", value)
mlflow.log_metric("best_tuned_score", tuning_result['best_score'])
# Evaluate tuned model
tuned_evaluation = ml_builder.evaluate_model(
tuning_result['best_model'], X_test, y_test,
f"{best_model_name}_tuned"
)
mlflow.log_metric("tuned_model_accuracy", tuned_evaluation['accuracy'])
if tuned_evaluation['roc_auc'] is not None:
mlflow.log_metric("tuned_model_roc_auc", tuned_evaluation['roc_auc'])
# Update best model if tuning improved performance
if tuned_evaluation['accuracy'] > best_score:
best_model = tuning_result['best_model']
best_score = tuned_evaluation['accuracy']
# Log feature importance
if tuned_evaluation['feature_importance']:
importance_json = json.dumps(tuned_evaluation['feature_importance'])
mlflow.log_text(importance_json, "feature_importance.json")
# Stage 5: Ensemble Creation
print("Stage 5: Creating ensemble models...")
try:
ensemble_results = ml_builder.ensemble_models(X_train, X_test, y_train, y_test)
for ensemble_type, result in ensemble_results.items():
if 'evaluation' in ensemble_type:
mlflow.log_metric(f"{ensemble_type}_accuracy", result['accuracy'])
if result['roc_auc'] is not None:
mlflow.log_metric(f"{ensemble_type}_roc_auc", result['roc_auc'])
except:
print("Ensemble creation failed, continuing...")
# Stage 6: Model Explainability
print("Stage 6: Generating model explanations...")
if best_model is not None:
explainability = ml_builder.model_explainability(best_model, X_test)
if 'shap_importance' in explainability:
shap_importance_json = json.dumps(explainability['shap_importance'])
mlflow.log_text(shap_importance_json, "shap_importance.json")
# Save final model
if save_models and best_model is not None:
model_path = f"models/{best_model_name}_final"
os.makedirs(model_path, exist_ok=True)
joblib.dump(best_model, f"{model_path}/model.joblib")
mlflow.log_artifact(f"{model_path}/model.joblib", "final_model")
# Generate pipeline report
pipeline_results = {
'run_id': self.run_id,
'experiment_id': self.experiment_id,
'data_info': data_info,
'best_model': best_model_name,
'best_score': best_score,
'model_results': {name: {'accuracy': result['accuracy'], 'cv_mean': result['cv_mean']}
for name, result in model_results.items()},
'timestamp': datetime.now().isoformat()
}
# Log pipeline results
results_json = json.dumps(pipeline_results, indent=2)
mlflow.log_text(results_json, "pipeline_results.json")
return pipeline_results
def _load_data(self, data_path: str) -> pd.DataFrame:
"""Load data from various formats"""
if data_path.endswith('.csv'):
return pd.read_csv(data_path)
elif data_path.endswith('.parquet'):
return pd.read_parquet(data_path)
elif data_path.endswith('.json'):
return pd.read_json(data_path)
else:
raise ValueError(f"Unsupported file format: {data_path}")
def _explore_data(self, df: pd.DataFrame) -> dict:
"""Basic data exploration"""
return {
'shape': df.shape,
'missing_values': df.isnull().sum().sum(),
'duplicate_rows': df.duplicated().sum(),
'numeric_columns': len(df.select_dtypes(include=[np.number]).columns),
'categorical_columns': len(df.select_dtypes(include=['object', 'category']).columns),
'memory_usage_mb': df.memory_usage(deep=True).sum() / 1024**2
}
def compare_experiments(self, metric: str = 'accuracy', top_k: int = 5) -> dict:
"""Compare multiple experiments"""
from mlflow.tracking import MlflowClient
client = MlflowClient()
runs = client.search_runs(
experiment_ids=[self.experiment_id],
order_by=[f"metrics.{metric} DESC"]
)
comparison_results = []
for run in runs[:top_k]:
run_data = {
'run_id': run.info.run_id,
'status': run.info.status,
'start_time': datetime.fromtimestamp(run.info.start_time / 1000),
'params': dict(run.data.params),
'metrics': dict(run.data.metrics)
}
comparison_results.append(run_data)
return {
'comparison_metric': metric,
'top_runs': comparison_results,
'total_runs': len(runs)
}
def deploy_model(self, run_id: str = None, model_name: str = "production_model") -> dict:
"""Prepare model for deployment"""
if run_id is None:
run_id = self.run_id
if run_id is None:
raise ValueError("No run ID provided and no current run found")
# Load model from MLflow
model_uri = f"runs:/{run_id}/final_model"
model = mlflow.sklearn.load_model(model_uri)
# Create deployment package
deployment_info = {
'model_uri': model_uri,
'run_id': run_id,
'model_name': model_name,
'deployment_timestamp': datetime.now().isoformat(),
'model_type': type(model).__name__
}
# Save deployment info
os.makedirs('deployment', exist_ok=True)
with open('deployment/deployment_info.json', 'w') as f:
json.dump(deployment_info, f, indent=2)
# Copy model to deployment directory
joblib.dump(model, 'deployment/model.joblib')
return deployment_info
# Usage example
# pipeline = ProductionMLPipeline("data_science_experiment")
# results = pipeline.run_complete_pipeline("data.csv", "target")
# comparison = pipeline.compare_experiments()
# deployment_info = pipeline.deploy_model()
Related Skills
- moai-domain-ml: Advanced machine learning techniques
- moai-domain-testing: Model testing and validation
- moai-document-processing: Data processing and extraction
- moai-essentials-refactor: Code optimization and performance
Quick Start Checklist
Data Science Best Practices
- Data Understanding: Always explore and understand your data first
- Preprocessing: Handle missing values, outliers, and feature engineering
- Statistical Validation: Use appropriate statistical tests and validation
- Model Selection: Try multiple algorithms and compare performance
- Cross-Validation: Use proper cross-validation techniques
- Hyperparameter Tuning: Optimize model parameters systematically
- Interpretability: Use SHAP, LIME for model explanations
- Experiment Tracking: Log all experiments for reproducibility
Data Science & Analytics - Build end-to-end data science solutions with comprehensive statistical analysis, machine learning, and experiment tracking capabilities.
