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Model loading and inference engine.
Loads XGBoost model, scaler, and SHAP explainer once at startup.
All prediction requests are handled through the Predictor class.
Design principle: load once, predict many times.
Loading a model on every request would be 10-100x slower.
"""
import joblib
import numpy as np
import pandas as pd
import shap
import logging
from pathlib import Path
from typing import Optional
from src.api.models import (
PatientFeatures,
PredictionResponse,
RiskCategory,
RiskFactor,
)
# Configure logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
# Feature order must match exactly what the model was trained on
# Any mismatch causes silent wrong predictions β worse than an error
FEATURE_ORDER = [
'los_days', 'los_days_log', 'admission_month', 'admission_dow',
'is_emergency', 'n_admissions_prior_6m', 'n_admissions_prior_12m',
'n_ed_visits_prior_6m', 'days_since_last_admission',
'has_prior_admission', 'charlson_score', 'n_active_conditions',
'has_heart_failure', 'has_diabetes', 'has_diabetes_complex',
'has_copd', 'has_ckd', 'has_mi', 'has_cancer', 'has_dementia',
'has_cerebrovascular', 'has_pvd', 'n_medications_capped',
'is_high_polypharmacy', 'has_insulin', 'has_anticoagulant',
'has_diuretic', 'has_ace_inhibitor', 'age_at_admission',
'gender_male', 'income',
]
# Clinical descriptions for each feature
# Used to generate plain-English explanations in the response
FEATURE_DESCRIPTIONS = {
'los_days': 'Length of hospital stay',
'los_days_log': 'Length of hospital stay (log scale)',
'admission_month': 'Month of admission',
'admission_dow': 'Day of week admitted',
'is_emergency': 'Emergency admission',
'n_admissions_prior_6m': 'Hospital admissions in past 6 months',
'n_admissions_prior_12m': 'Hospital admissions in past 12 months',
'n_ed_visits_prior_6m': 'Emergency department visits in past 6 months',
'days_since_last_admission': 'Days since last hospital admission',
'has_prior_admission': 'History of prior hospitalisation',
'charlson_score': 'Charlson Comorbidity Index score',
'n_active_conditions': 'Number of active medical conditions',
'has_heart_failure': 'Heart failure diagnosis',
'has_diabetes': 'Diabetes mellitus diagnosis',
'has_diabetes_complex': 'Diabetes with complications',
'has_copd': 'Chronic obstructive pulmonary disease',
'has_ckd': 'Chronic kidney disease',
'has_mi': 'History of myocardial infarction',
'has_cancer': 'Active cancer diagnosis',
'has_dementia': 'Dementia diagnosis',
'has_cerebrovascular': 'Cerebrovascular disease',
'has_pvd': 'Peripheral vascular disease',
'n_medications_capped': 'Number of active medications',
'is_high_polypharmacy': 'High polypharmacy (>10 medications)',
'has_insulin': 'Insulin therapy',
'has_anticoagulant': 'Anticoagulant therapy',
'has_diuretic': 'Diuretic therapy',
'has_ace_inhibitor': 'ACE inhibitor therapy',
'age_at_admission': 'Patient age at admission',
'gender_male': 'Male gender',
'income': 'Household income',
}
# Risk thresholds β calibrated to our model's output distribution
# LOW: < 20% β standard discharge
# MEDIUM: 20-50% β enhanced follow-up
# HIGH: > 50% β intensive intervention
RISK_THRESHOLDS = {
'LOW': 0.20,
'MEDIUM': 0.50,
}
# Clinical recommendations by risk category
RECOMMENDATIONS = {
RiskCategory.LOW: (
"Standard discharge protocol. "
"Schedule routine 30-day follow-up appointment. "
"Provide patient with discharge summary and medication list."
),
RiskCategory.MEDIUM: (
"Enhanced discharge protocol. "
"Schedule 14-day follow-up appointment. "
"Conduct pharmacist medication reconciliation. "
"Provide patient education on warning signs requiring ED return."
),
RiskCategory.HIGH: (
"High-risk discharge protocol. "
"Schedule 7-day follow-up appointment. "
"Assign care coordinator for post-discharge monitoring. "
"Conduct pharmacist medication reconciliation before discharge. "
"Consider social work referral if social support is limited. "
"Confirm patient has transport and medication access post-discharge."
),
}
class Predictor:
"""
Manages model lifecycle and inference.
Loaded once at API startup via FastAPI lifespan events.
Thread-safe for concurrent requests β models are read-only after loading.
"""
def __init__(self, models_path: str = "models"):
self.models_path = Path(models_path)
self.model = None
self.scaler = None
self.explainer = None
self.model_version = "xgboost_v1_auc0.891"
self._loaded = False
def load(self) -> None:
"""
Load model, scaler, and SHAP explainer from disk.
Called once at API startup β not on every request.
"""
logger.info("Loading model artifacts...")
try:
# Load XGBoost model
model_path = self.models_path / "xgboost_model.pkl"
self.model = joblib.load(model_path)
logger.info(f"Model loaded from {model_path}")
# Load scaler β must be the same scaler used in training
scaler_path = self.models_path / "scaler.pkl"
self.scaler = joblib.load(scaler_path)
logger.info(f"Scaler loaded from {scaler_path}")
# Build SHAP explainer β TreeExplainer for XGBoost
# This is slow to build (~5s) but fast to query
self.explainer = shap.TreeExplainer(self.model)
logger.info("SHAP explainer ready")
self._loaded = True
logger.info(
f"All artifacts loaded successfully. "
f"Model version: {self.model_version}"
)
except FileNotFoundError as e:
logger.error(f"Model file not found: {e}")
raise
except Exception as e:
logger.error(f"Failed to load model: {e}")
raise
@property
def is_loaded(self) -> bool:
return self._loaded
def _features_to_array(
self, features: PatientFeatures
) -> pd.DataFrame:
"""Convert Pydantic model to DataFrame in correct feature order."""
feature_dict = features.model_dump()
ordered = {f: [feature_dict[f]] for f in FEATURE_ORDER}
return pd.DataFrame(ordered)
def _get_risk_category(
self, probability: float
) -> RiskCategory:
"""Map probability to clinical risk category."""
if probability < RISK_THRESHOLDS['LOW']:
return RiskCategory.LOW
elif probability < RISK_THRESHOLDS['MEDIUM']:
return RiskCategory.MEDIUM
else:
return RiskCategory.HIGH
def _compute_shap_factors(
self,
raw_array: np.ndarray,
features: PatientFeatures,
top_n: int = 5
) -> list[RiskFactor]:
"""
Compute SHAP values and return top N risk factors
with clinical plain-English descriptions.
"""
shap_values = self.explainer.shap_values(raw_array)[0]
feature_dict = features.model_dump()
# Build list of (feature, value, shap_value)
factors = [
(feat, feature_dict[feat], shap_val)
for feat, shap_val in zip(FEATURE_ORDER, shap_values)
]
# Sort by absolute SHAP value β largest impact first
factors_sorted = sorted(
factors, key=lambda x: abs(x[2]), reverse=True
)[:top_n]
risk_factors = []
for feat, val, shap_val in factors_sorted:
risk_factors.append(RiskFactor(
feature=feat,
value=round(float(val), 3),
impact=round(float(shap_val), 4),
direction="increases" if shap_val > 0 else "decreases",
description=FEATURE_DESCRIPTIONS.get(feat, feat)
))
return risk_factors
def predict(self, features: PatientFeatures) -> PredictionResponse:
"""
Run full prediction pipeline for one patient.
Steps:
1. Convert features to array in correct order
2. Scale features using training scaler
3. Get probability from XGBoost
4. Compute SHAP values for explainability
5. Build structured clinical response
Returns:
PredictionResponse with risk score, category,
SHAP factors, and clinical recommendation
"""
if not self._loaded:
raise RuntimeError(
"Model not loaded. Call predictor.load() first."
)
# Step 1 β features to array
raw_df = self._features_to_array(features)
# Step 2 β scale
scaled_array = self.scaler.transform(raw_df)
# Step 3 β predict probability
probability = float(
self.model.predict_proba(scaled_array)[0][1]
)
# Step 4 β SHAP explanation
risk_factors = self._compute_shap_factors(
scaled_array, features, top_n=5
)
# Step 5 β build response
risk_category = self._get_risk_category(probability)
risk_percent = round(probability * 100, 1)
return PredictionResponse(
readmission_risk = round(probability, 4),
risk_percent = risk_percent,
risk_category = risk_category,
risk_score_display = f"{risk_percent}% readmission risk",
top_risk_factors = risk_factors,
recommendation = RECOMMENDATIONS[risk_category],
model_version = self.model_version,
)
# Global predictor instance
# Imported by routers β loaded once at startup
predictor = Predictor() |