Data-Science-Agent / src /tools /advanced_analysis.py
Pulastya B
fix: Fix module import paths for Render deployment
227cb22
"""
Advanced Analysis Tools
Tools for EDA, model diagnostics, anomaly detection, multicollinearity, and statistical tests.
"""
import polars as pl
import numpy as np
from typing import Dict, Any, List, Optional, Tuple
from pathlib import Path
import sys
import os
import warnings
import json
warnings.filterwarnings('ignore')
# Add parent directory to path for imports
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from sklearn.ensemble import IsolationForest
from sklearn.neighbors import LocalOutlierFactor
from sklearn.model_selection import learning_curve
from scipy import stats
from scipy.stats import chi2_contingency, f_oneway, ttest_ind, pearsonr
from statsmodels.stats.outliers_influence import variance_inflation_factor
import plotly.graph_objects as go
import plotly.express as px
from plotly.subplots import make_subplots
import pandas as pd
from ..utils.polars_helpers import (
load_dataframe, get_numeric_columns, get_categorical_columns
)
from ..utils.validation import (
validate_file_exists, validate_file_format, validate_dataframe,
validate_column_exists
)
def perform_eda_analysis(
file_path: str,
target_col: Optional[str] = None,
output_html: Optional[str] = None
) -> Dict[str, Any]:
"""
Perform comprehensive automated Exploratory Data Analysis with interactive visualizations.
Args:
file_path: Path to dataset
target_col: Target column for supervised analysis
output_html: Path to save HTML report
Returns:
Dictionary with EDA insights and statistics
"""
# Validation
validate_file_exists(file_path)
validate_file_format(file_path)
# Load data
df = load_dataframe(file_path)
validate_dataframe(df)
if target_col:
validate_column_exists(df, target_col)
print("📊 Performing comprehensive EDA...")
# Basic statistics
n_rows, n_cols = df.shape
numeric_cols = get_numeric_columns(df)
categorical_cols = get_categorical_columns(df)
# Missing values analysis
missing_stats = {}
for col in df.columns:
null_count = df[col].null_count()
if null_count > 0:
missing_stats[col] = {
'count': null_count,
'percentage': float(null_count / n_rows * 100)
}
# Univariate analysis for numeric columns
numeric_stats = {}
for col in numeric_cols[:20]: # Limit to 20 columns
col_data = df[col].drop_nulls().to_numpy()
numeric_stats[col] = {
'mean': float(np.mean(col_data)),
'median': float(np.median(col_data)),
'std': float(np.std(col_data)),
'min': float(np.min(col_data)),
'max': float(np.max(col_data)),
'q25': float(np.percentile(col_data, 25)),
'q75': float(np.percentile(col_data, 75)),
'skewness': float(stats.skew(col_data)),
'kurtosis': float(stats.kurtosis(col_data))
}
# Categorical analysis
categorical_stats = {}
for col in categorical_cols[:10]: # Limit to 10 columns
value_counts = df[col].value_counts().head(10)
categorical_stats[col] = {
'unique_values': df[col].n_unique(),
'mode': df[col].mode()[0] if len(df[col].mode()) > 0 else None,
'top_10_values': {str(row[col]): row['count'] for row in value_counts.to_dicts()}
}
# Correlation analysis (numeric only)
correlations = {}
if len(numeric_cols) > 1:
corr_matrix = df[numeric_cols[:20]].to_pandas().corr()
# Find highly correlated pairs
high_corr_pairs = []
for i in range(len(corr_matrix.columns)):
for j in range(i+1, len(corr_matrix.columns)):
corr_val = corr_matrix.iloc[i, j]
if abs(corr_val) > 0.7:
high_corr_pairs.append({
'feature_1': corr_matrix.columns[i],
'feature_2': corr_matrix.columns[j],
'correlation': float(corr_val)
})
correlations['high_correlations'] = high_corr_pairs
correlations['correlation_matrix_shape'] = corr_matrix.shape
# Target analysis
target_insights = {}
if target_col:
if target_col in numeric_cols:
# Numeric target - regression
target_data = df[target_col].drop_nulls().to_numpy()
target_insights = {
'type': 'regression',
'mean': float(np.mean(target_data)),
'std': float(np.std(target_data)),
'min': float(np.min(target_data)),
'max': float(np.max(target_data))
}
# Feature-target correlations
target_corr = {}
for col in numeric_cols:
if col != target_col:
try:
corr, pval = pearsonr(
df[col].drop_nulls().to_numpy(),
df[target_col].drop_nulls().to_numpy()
)
if abs(corr) > 0.3:
target_corr[col] = {
'correlation': float(corr),
'p_value': float(pval)
}
except:
pass
target_insights['correlated_features'] = target_corr
else:
# Categorical target - classification
value_counts = df[target_col].value_counts()
target_insights = {
'type': 'classification',
'classes': len(value_counts),
'distribution': {str(row[target_col]): row['count'] for row in value_counts.to_dicts()},
'imbalance_ratio': float(value_counts['count'].max() / value_counts['count'].min())
}
# Create visualizations if output_html requested
if output_html:
print("📈 Generating interactive visualizations...")
fig = make_subplots(
rows=3, cols=2,
subplot_titles=('Distribution of Numeric Features', 'Missing Values',
'Correlation Heatmap', 'Target Distribution',
'Outliers Detection', 'Feature Importance')
)
# Distribution plot (first numeric column)
if numeric_cols:
col = numeric_cols[0]
fig.add_trace(
go.Histogram(x=df[col].to_list(), name=col),
row=1, col=1
)
# Missing values plot
if missing_stats:
missing_cols = list(missing_stats.keys())[:10]
missing_pcts = [missing_stats[col]['percentage'] for col in missing_cols]
fig.add_trace(
go.Bar(x=missing_cols, y=missing_pcts, name='Missing %'),
row=1, col=2
)
# Correlation heatmap
if len(numeric_cols) > 1:
corr_matrix_np = corr_matrix.values
fig.add_trace(
go.Heatmap(
z=corr_matrix_np,
x=corr_matrix.columns.tolist(),
y=corr_matrix.columns.tolist(),
colorscale='RdBu'
),
row=2, col=1
)
# Target distribution
if target_col and target_col in categorical_cols:
target_counts = df[target_col].value_counts()
fig.add_trace(
go.Bar(
x=[str(row[target_col]) for row in target_counts.to_dicts()],
y=[row['count'] for row in target_counts.to_dicts()],
name='Target'
),
row=2, col=2
)
fig.update_layout(height=1200, showlegend=False, title_text="Automated EDA Report")
# Save HTML
os.makedirs(os.path.dirname(output_html) if os.path.dirname(output_html) else '.', exist_ok=True)
fig.write_html(output_html)
print(f"💾 EDA report saved to: {output_html}")
return {
'status': 'success',
'dataset_shape': {'rows': n_rows, 'columns': n_cols},
'column_types': {
'numeric': len(numeric_cols),
'categorical': len(categorical_cols)
},
'missing_values': missing_stats,
'numeric_statistics': numeric_stats,
'categorical_statistics': categorical_stats,
'correlations': correlations,
'target_insights': target_insights,
'output_html': output_html
}
def detect_model_issues(
model_path: str,
train_data_path: str,
test_data_path: str,
target_col: str
) -> Dict[str, Any]:
"""
Detect overfitting, underfitting, and other model issues using learning curves and diagnostics.
Args:
model_path: Path to trained model (.pkl)
train_data_path: Path to training dataset
test_data_path: Path to test dataset
target_col: Target column name
Returns:
Dictionary with model diagnostics
"""
import joblib
from sklearn.metrics import accuracy_score, mean_squared_error, r2_score
# Validation
validate_file_exists(model_path)
validate_file_exists(train_data_path)
validate_file_exists(test_data_path)
# Load model
model = joblib.load(model_path)
# Load data
train_df = load_dataframe(train_data_path)
test_df = load_dataframe(test_data_path)
validate_column_exists(train_df, target_col)
validate_column_exists(test_df, target_col)
# Prepare data
from utils.polars_helpers import split_features_target
X_train, y_train = split_features_target(train_df, target_col)
X_test, y_test = split_features_target(test_df, target_col)
print("🔍 Analyzing model performance...")
# Predictions
y_train_pred = model.predict(X_train)
y_test_pred = model.predict(X_test)
# Detect task type
unique_values = len(np.unique(y_train))
task_type = "classification" if unique_values < 20 else "regression"
# Calculate metrics
if task_type == "classification":
train_score = accuracy_score(y_train, y_train_pred)
test_score = accuracy_score(y_test, y_test_pred)
metric_name = "accuracy"
else:
train_score = r2_score(y_train, y_train_pred)
test_score = r2_score(y_test, y_test_pred)
metric_name = "r2"
# Diagnose issues
score_gap = train_score - test_score
diagnosis = []
if score_gap > 0.15:
diagnosis.append({
'issue': 'overfitting',
'severity': 'high' if score_gap > 0.25 else 'medium',
'description': f'Training {metric_name} ({train_score:.3f}) is much higher than test {metric_name} ({test_score:.3f})',
'recommendations': [
'Add regularization (L1/L2)',
'Reduce model complexity',
'Increase training data',
'Use cross-validation',
'Add dropout (for neural networks)'
]
})
if test_score < 0.6 and task_type == "classification":
diagnosis.append({
'issue': 'underfitting',
'severity': 'high',
'description': f'Test accuracy ({test_score:.3f}) is too low',
'recommendations': [
'Increase model complexity',
'Engineer better features',
'Try ensemble methods',
'Tune hyperparameters',
'Check for data quality issues'
]
})
if test_score < 0.3 and task_type == "regression":
diagnosis.append({
'issue': 'underfitting',
'severity': 'high',
'description': f'Test R² ({test_score:.3f}) is too low',
'recommendations': [
'Increase model complexity',
'Engineer better features',
'Try non-linear models',
'Check for data scaling issues'
]
})
# Bias-variance analysis
if abs(score_gap) < 0.05:
bias_variance = 'balanced'
elif score_gap > 0.15:
bias_variance = 'high_variance' # Overfitting
else:
bias_variance = 'high_bias' # Underfitting
# Generate learning curve data
print("📊 Generating learning curve...")
try:
train_sizes = np.linspace(0.1, 1.0, 10)
train_sizes_abs, train_scores, val_scores = learning_curve(
model, X_train, y_train,
train_sizes=train_sizes,
cv=5,
scoring='accuracy' if task_type == "classification" else 'r2',
n_jobs=-1
)
learning_curve_data = {
'train_sizes': train_sizes_abs.tolist(),
'train_scores_mean': train_scores.mean(axis=1).tolist(),
'val_scores_mean': val_scores.mean(axis=1).tolist()
}
except Exception as e:
learning_curve_data = {'error': str(e)}
return {
'status': 'success',
'task_type': task_type,
'train_score': float(train_score),
'test_score': float(test_score),
'score_gap': float(score_gap),
'bias_variance_assessment': bias_variance,
'diagnosis': diagnosis,
'learning_curve': learning_curve_data,
'summary': f"Model shows {bias_variance} with {len(diagnosis)} issues detected"
}
def detect_anomalies(
file_path: str,
method: str = "isolation_forest",
contamination: float = 0.1,
columns: Optional[List[str]] = None,
output_path: Optional[str] = None
) -> Dict[str, Any]:
"""
Detect anomalies/outliers using various methods.
Args:
file_path: Path to dataset
method: Anomaly detection method:
- 'isolation_forest': Isolation Forest (good for high-dim data)
- 'lof': Local Outlier Factor
- 'zscore': Z-score method (univariate)
- 'iqr': Interquartile Range method (univariate)
contamination: Expected proportion of outliers (0.01 to 0.5)
columns: Columns to analyze (None = all numeric)
output_path: Path to save dataset with anomaly labels
Returns:
Dictionary with anomaly detection results
"""
# Validation
validate_file_exists(file_path)
validate_file_format(file_path)
# Load data
df = load_dataframe(file_path)
validate_dataframe(df)
# Get numeric columns if not specified
if columns is None:
columns = get_numeric_columns(df)
print(f"🔢 Auto-detected {len(columns)} numeric columns")
else:
for col in columns:
validate_column_exists(df, col)
if not columns:
return {
'status': 'skipped',
'message': 'No numeric columns found for anomaly detection'
}
X = df[columns].fill_null(0).to_numpy()
print(f"🔍 Detecting anomalies using {method}...")
# Detect anomalies based on method
if method == "isolation_forest":
detector = IsolationForest(contamination=contamination, random_state=42, n_jobs=-1)
predictions = detector.fit_predict(X)
anomaly_scores = detector.score_samples(X)
anomalies = predictions == -1
elif method == "lof":
detector = LocalOutlierFactor(contamination=contamination, n_jobs=-1)
predictions = detector.fit_predict(X)
anomaly_scores = detector.negative_outlier_factor_
anomalies = predictions == -1
elif method == "zscore":
# Z-score for each column
z_scores = np.abs(stats.zscore(X, axis=0))
anomalies = (z_scores > 3).any(axis=1)
anomaly_scores = z_scores.max(axis=1)
elif method == "iqr":
# IQR for each column
Q1 = np.percentile(X, 25, axis=0)
Q3 = np.percentile(X, 75, axis=0)
IQR = Q3 - Q1
lower_bound = Q1 - 1.5 * IQR
upper_bound = Q3 + 1.5 * IQR
anomalies = ((X < lower_bound) | (X > upper_bound)).any(axis=1)
# Calculate how many IQRs away from bounds
dist_from_bounds = np.maximum(
(lower_bound - X) / IQR,
(X - upper_bound) / IQR
).max(axis=1)
anomaly_scores = dist_from_bounds
else:
raise ValueError(f"Unsupported method: {method}")
# Count anomalies
n_anomalies = int(anomalies.sum())
anomaly_percentage = float(n_anomalies / len(df) * 100)
print(f"🚨 Found {n_anomalies} anomalies ({anomaly_percentage:.2f}%)")
# Add anomaly labels to dataframe
df_with_anomalies = df.with_columns([
pl.Series('is_anomaly', anomalies.astype(int)),
pl.Series('anomaly_score', anomaly_scores)
])
# Get indices of anomalies
anomaly_indices = np.where(anomalies)[0].tolist()
# Analyze anomalies by column
column_anomaly_stats = {}
for col in columns:
col_data = df[col].to_numpy()
anomaly_values = col_data[anomalies]
if len(anomaly_values) > 0:
column_anomaly_stats[col] = {
'mean_normal': float(np.mean(col_data[~anomalies])),
'mean_anomaly': float(np.mean(anomaly_values)),
'std_normal': float(np.std(col_data[~anomalies])),
'std_anomaly': float(np.std(anomaly_values))
}
# Save if output path provided
if output_path:
from utils.polars_helpers import save_dataframe
save_dataframe(df_with_anomalies, output_path)
print(f"💾 Dataset with anomaly labels saved to: {output_path}")
return {
'status': 'success',
'method': method,
'n_anomalies': n_anomalies,
'anomaly_percentage': anomaly_percentage,
'anomaly_indices': anomaly_indices[:100], # First 100
'column_statistics': column_anomaly_stats,
'contamination': contamination,
'output_path': output_path
}
def detect_and_handle_multicollinearity(
file_path: str,
threshold: float = 10.0,
action: str = "report",
output_path: Optional[str] = None
) -> Dict[str, Any]:
"""
Detect and optionally handle multicollinearity using VIF (Variance Inflation Factor).
Args:
file_path: Path to dataset
threshold: VIF threshold (10 = high multicollinearity, 5 = moderate)
action: Action to take:
- 'report': Only report VIF values
- 'remove': Remove features with VIF > threshold
- 'recommend': Provide regularization recommendations
output_path: Path to save dataset with reduced features
Returns:
Dictionary with VIF values and recommendations
"""
# Validation
validate_file_exists(file_path)
validate_file_format(file_path)
# Load data
df = load_dataframe(file_path)
validate_dataframe(df)
# Get numeric columns
numeric_cols = get_numeric_columns(df)
if len(numeric_cols) < 2:
return {
'status': 'skipped',
'message': 'Need at least 2 numeric columns for multicollinearity analysis'
}
print(f"🔍 Calculating VIF for {len(numeric_cols)} features...")
# Prepare data
X = df[numeric_cols].fill_null(0).to_numpy()
# Calculate VIF for each feature
vif_data = {}
problematic_features = []
for i, col in enumerate(numeric_cols):
try:
vif = variance_inflation_factor(X, i)
vif_data[col] = float(vif)
if vif > threshold:
problematic_features.append({
'feature': col,
'vif': float(vif),
'severity': 'high' if vif > 20 else 'moderate'
})
except Exception as e:
vif_data[col] = None
print(f"⚠️ Could not calculate VIF for {col}: {str(e)}")
# Sort by VIF
sorted_vif = dict(sorted(vif_data.items(), key=lambda x: x[1] if x[1] is not None else 0, reverse=True))
# Generate recommendations
recommendations = []
if len(problematic_features) > 0:
recommendations.append({
'type': 'regularization',
'description': 'Use Ridge (L2) or Elastic Net regularization to handle multicollinearity',
'reason': f'{len(problematic_features)} features have VIF > {threshold}'
})
recommendations.append({
'type': 'pca',
'description': 'Apply PCA to reduce dimensionality and eliminate correlations',
'reason': 'PCA creates orthogonal features'
})
if action == "remove":
# Remove features with highest VIF iteratively
features_to_remove = [f['feature'] for f in problematic_features]
recommendations.append({
'type': 'feature_removal',
'description': f'Remove {len(features_to_remove)} features with high VIF',
'features': features_to_remove
})
# Handle action
if action == "remove" and len(problematic_features) > 0:
# Remove features with VIF > threshold
features_to_keep = [col for col in numeric_cols if col not in [f['feature'] for f in problematic_features]]
categorical_cols = get_categorical_columns(df)
df_reduced = df.select(features_to_keep + categorical_cols)
if output_path:
from utils.polars_helpers import save_dataframe
save_dataframe(df_reduced, output_path)
print(f"💾 Dataset with reduced features saved to: {output_path}")
return {
'status': 'success',
'action': 'removed',
'vif_values': sorted_vif,
'problematic_features': problematic_features,
'features_removed': len(problematic_features),
'features_remaining': len(features_to_keep),
'recommendations': recommendations,
'output_path': output_path
}
return {
'status': 'success',
'action': action,
'vif_values': sorted_vif,
'problematic_features': problematic_features,
'threshold': threshold,
'recommendations': recommendations
}
def perform_statistical_tests(
file_path: str,
target_col: str,
test_type: str = "auto",
features: Optional[List[str]] = None,
alpha: float = 0.05
) -> Dict[str, Any]:
"""
Perform statistical hypothesis tests to validate feature relationships.
Args:
file_path: Path to dataset
target_col: Target column name
test_type: Type of test:
- 'auto': Automatically select based on data types
- 'chi2': Chi-square test (categorical vs categorical)
- 'ttest': T-test (binary categorical vs numeric)
- 'anova': ANOVA (multi-class categorical vs numeric)
- 'pearson': Pearson correlation test (numeric vs numeric)
features: Features to test (None = all)
alpha: Significance level (default 0.05)
Returns:
Dictionary with test results and p-values
"""
# Validation
validate_file_exists(file_path)
validate_file_format(file_path)
# Load data
df = load_dataframe(file_path)
validate_dataframe(df)
validate_column_exists(df, target_col)
# Get column types
numeric_cols = get_numeric_columns(df)
categorical_cols = get_categorical_columns(df)
# Determine target type
target_is_numeric = target_col in numeric_cols
target_is_categorical = target_col in categorical_cols
# Get features to test
if features is None:
features = [col for col in df.columns if col != target_col]
print(f"📊 Performing statistical tests for {len(features)} features...")
test_results = []
for feature in features:
feature_is_numeric = feature in numeric_cols
feature_is_categorical = feature in categorical_cols
# Skip if feature is target
if feature == target_col:
continue
# Select appropriate test
if test_type == "auto":
if target_is_numeric and feature_is_numeric:
selected_test = "pearson"
elif target_is_categorical and feature_is_numeric:
target_unique = df[target_col].n_unique()
selected_test = "ttest" if target_unique == 2 else "anova"
elif target_is_categorical and feature_is_categorical:
selected_test = "chi2"
elif target_is_numeric and feature_is_categorical:
selected_test = "anova"
else:
continue
else:
selected_test = test_type
# Perform test
try:
if selected_test == "pearson":
# Pearson correlation
feature_data = df[feature].drop_nulls().to_numpy()
target_data = df[target_col].drop_nulls().to_numpy()
# Align lengths
min_len = min(len(feature_data), len(target_data))
corr, pval = pearsonr(feature_data[:min_len], target_data[:min_len])
test_results.append({
'feature': feature,
'test': 'pearson',
'statistic': float(corr),
'p_value': float(pval),
'significant': pval < alpha,
'interpretation': f"Correlation: {corr:.3f}"
})
elif selected_test == "chi2":
# Chi-square test
contingency_table = pd.crosstab(
df[feature].to_pandas(),
df[target_col].to_pandas()
)
chi2, pval, dof, expected = chi2_contingency(contingency_table)
test_results.append({
'feature': feature,
'test': 'chi2',
'statistic': float(chi2),
'p_value': float(pval),
'dof': int(dof),
'significant': pval < alpha
})
elif selected_test == "ttest":
# T-test
target_values = df[target_col].unique().to_list()
if len(target_values) != 2:
continue
group1 = df.filter(pl.col(target_col) == target_values[0])[feature].drop_nulls().to_numpy()
group2 = df.filter(pl.col(target_col) == target_values[1])[feature].drop_nulls().to_numpy()
t_stat, pval = ttest_ind(group1, group2)
test_results.append({
'feature': feature,
'test': 'ttest',
'statistic': float(t_stat),
'p_value': float(pval),
'significant': pval < alpha,
'mean_diff': float(np.mean(group1) - np.mean(group2))
})
elif selected_test == "anova":
# ANOVA
groups = []
target_values = df[target_col].unique().to_list()
for val in target_values:
group_data = df.filter(pl.col(target_col) == val)[feature].drop_nulls().to_numpy()
if len(group_data) > 0:
groups.append(group_data)
if len(groups) > 1:
f_stat, pval = f_oneway(*groups)
test_results.append({
'feature': feature,
'test': 'anova',
'statistic': float(f_stat),
'p_value': float(pval),
'significant': pval < alpha,
'n_groups': len(groups)
})
except Exception as e:
print(f"⚠️ Test failed for {feature}: {str(e)}")
# Summary
significant_features = [r for r in test_results if r['significant']]
print(f"✅ {len(significant_features)}/{len(test_results)} features are statistically significant (α={alpha})")
return {
'status': 'success',
'target_column': target_col,
'alpha': alpha,
'total_tests': len(test_results),
'significant_features': len(significant_features),
'test_results': test_results,
'significant_features_list': [r['feature'] for r in significant_features]
}