iints-sdk-python35 0.1.18__tar.gz → 0.1.20__tar.gz

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iints-sdk-python35
-Version: 0.1.18
+Version: 0.1.20
 Summary: A pre-clinical Edge-AI SDK for diabetes management validation.
 Author-email: Rune Bobbaers <rune.bobbaers@gmail.com>
 Project-URL: Homepage, https://github.com/python35/IINTS-SDK
@@ -29,6 +29,7 @@ Requires-Dist: seaborn>=0.11.0
 Requires-Dist: typer[all]
 Provides-Extra: dev
 Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: hypothesis>=6.0.0; extra == "dev"
 Requires-Dist: flake8; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pandas-stubs; extra == "dev"
@@ -206,7 +207,9 @@ outputs = iints.run_simulation(..., predictor=predictor)
 ```
 
 ### Documentation
-* Product manual: `docs/COMPREHENSIVE_GUIDE.md`
+* PDF manual: `docs/manuals/IINTS-AF_SDK_Manual.pdf`
+* Manual source: `docs/manuals/IINTS-AF_SDK_Manual.md`
+* Comprehensive guide: `docs/COMPREHENSIVE_GUIDE.md`
 * Notebook index: `examples/notebooks/README.md`
 * Technical README: `docs/TECHNICAL_README.md`
 * API Stability: `API_STABILITY.md`

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/README.md

@@ -158,7 +158,9 @@ outputs = iints.run_simulation(..., predictor=predictor)
 ```
 
 ### Documentation
-* Product manual: `docs/COMPREHENSIVE_GUIDE.md`
+* PDF manual: `docs/manuals/IINTS-AF_SDK_Manual.pdf`
+* Manual source: `docs/manuals/IINTS-AF_SDK_Manual.md`
+* Comprehensive guide: `docs/COMPREHENSIVE_GUIDE.md`
 * Notebook index: `examples/notebooks/README.md`
 * Technical README: `docs/TECHNICAL_README.md`
 * API Stability: `API_STABILITY.md`

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "0.1.18"
+version = "0.1.20"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
@@ -39,6 +39,7 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
   "pytest>=7.0.0",
+  "hypothesis>=6.0.0",
   "flake8",
   "mypy",
   "pandas-stubs",

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/__init__.py

@@ -3,7 +3,7 @@
 import pandas as pd # Required for type hints like pd.DataFrame
 from typing import Optional
 
-__version__ = "0.1.18"
+__version__ = "0.1.20"
 
 # Note to developers: this SDK is currently maintained by a single author.
 # Please report bugs via GitHub issues and feel free to contribute fixes via PRs.
@@ -20,6 +20,7 @@ from .api.base_algorithm import (
 # Core Simulation Components
 from .core.simulator import Simulator, StressEvent, SimulationLimitError
 from .core.patient.models import PatientModel
+from .core.patient.patient_factory import PatientFactory
 from .core.patient.profile import PatientProfile
 try:
     from .core.device_manager import DeviceManager
@@ -130,6 +131,7 @@ __all__ = [
     "InsulinAlgorithm", "AlgorithmInput", "AlgorithmResult", "AlgorithmMetadata", "WhyLogEntry",
     # Core
     "Simulator", "StressEvent", "PatientModel", "DeviceManager",
+    "PatientFactory",
     "PatientProfile",
     "SimulationLimitError",
     "SafetySupervisor",

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/cli/cli.py

@@ -226,7 +226,7 @@ def evaluate(
     output_dir: Annotated[Optional[Path], typer.Option(help="Output directory")] = None,
     max_workers: Annotated[Optional[int], typer.Option(help="Max parallel workers (default: all cores)")] = None,
     seed: Annotated[Optional[int], typer.Option(help="Random seed for reproducibility")] = None,
-    patient_model: Annotated[str, typer.Option("--patient-model", help="Patient model type: 'custom' or 'bergman'")] = "custom",
+    patient_model: Annotated[str, typer.Option("--patient-model", help="Patient model: auto, bergman, custom, simglucose")] = "auto",
 ):
     """
     Run a Monte Carlo population evaluation of an algorithm.
@@ -581,6 +581,11 @@ def presets_run(
     output_dir: Annotated[Optional[Path], typer.Option(help="Directory to save outputs")] = None,
     compare_baselines: Annotated[bool, typer.Option(help="Run PID and standard pump baselines in the background")] = True,
     seed: Annotated[Optional[int], typer.Option(help="Random seed for deterministic runs")] = None,
+    patient_model_type: Annotated[str, typer.Option("--patient-model", help="Patient model: auto, bergman, custom, simglucose")] = "auto",
+    sensor_noise_std: Annotated[Optional[float], typer.Option("--sensor-noise-std", help="CGM noise std (mg/dL)")] = None,
+    sensor_lag_minutes: Annotated[Optional[int], typer.Option("--sensor-lag-minutes", help="CGM lag (minutes)")] = None,
+    sensor_dropout_prob: Annotated[Optional[float], typer.Option("--sensor-dropout-prob", help="CGM dropout probability (0-1)")] = None,
+    sensor_bias: Annotated[Optional[float], typer.Option("--sensor-bias", help="CGM bias (mg/dL)")] = None,
     safety_min_glucose: Annotated[Optional[float], typer.Option("--safety-min-glucose", help="Min plausible glucose (mg/dL)")] = None,
     safety_max_glucose: Annotated[Optional[float], typer.Option("--safety-max-glucose", help="Max plausible glucose (mg/dL)")] = None,
     safety_max_glucose_delta_per_5_min: Annotated[Optional[float], typer.Option("--safety-max-glucose-delta-per-5-min", help="Max glucose delta per 5 min (mg/dL)")] = None,
@@ -613,7 +618,7 @@ def presets_run(
     try:
         patient_config_name = preset.get("patient_config", "default_patient")
         validated_patient_params = load_patient_config_by_name(patient_config_name).model_dump()
-        patient_model = iints.PatientModel(**validated_patient_params)
+        patient_model = iints.PatientFactory.create_patient(patient_type=patient_model_type, **validated_patient_params)
     except ValidationError as e:
         console.print("[bold red]Patient config validation failed:[/bold red]")
         for line in format_validation_error(e):
@@ -642,12 +647,32 @@ def presets_run(
         critical_glucose_duration_minutes=safety_critical_glucose_duration_minutes,
     )
 
+    sensor_model = None
+    if any(v is not None for v in (sensor_noise_std, sensor_lag_minutes, sensor_dropout_prob, sensor_bias)):
+        sensor_model = iints.SensorModel(
+            noise_std=float(sensor_noise_std or 0.0),
+            lag_minutes=int(sensor_lag_minutes or 0),
+            dropout_prob=float(sensor_dropout_prob or 0.0),
+            bias=float(sensor_bias or 0.0),
+            seed=resolved_seed,
+        )
+    elif patient_model_type == "auto":
+        sensor_model = iints.SensorModel(
+            noise_std=7.0,
+            lag_minutes=10,
+            dropout_prob=0.0,
+            bias=0.0,
+            seed=resolved_seed,
+        )
+
     simulator_kwargs: Dict[str, Any] = {
         "patient_model": patient_model,
         "algorithm": algorithm_instance,
         "time_step": time_step,
         "safety_config": safety_config,
     }
+    if sensor_model is not None:
+        simulator_kwargs["sensor_model"] = sensor_model
     simulator_kwargs["seed"] = resolved_seed
     if safety_config is None:
         safety_config = SafetyConfig()
@@ -740,8 +765,9 @@ def presets_run(
     if compare_baselines:
         manifest_files["baseline_json"] = output_dir / "baseline" / "baseline_comparison.json"
         manifest_files["baseline_csv"] = output_dir / "baseline" / "baseline_comparison.csv"
-    if output_dir / "audit" / "audit_summary.json":
-        manifest_files["audit_summary"] = output_dir / "audit" / "audit_summary.json"
+    audit_summary_path = output_dir / "audit" / "audit_summary.json"
+    if audit_summary_path.exists():
+        manifest_files["audit_summary"] = audit_summary_path
     run_manifest = build_run_manifest(output_dir, manifest_files)
     run_manifest_path = output_dir / "run_manifest.json"
     write_json(run_manifest_path, run_manifest)
@@ -749,9 +775,6 @@ def presets_run(
     signature_path = maybe_sign_manifest(run_manifest_path)
     if signature_path:
         console.print(f"Run manifest signature: {signature_path}")
-    signature_path = maybe_sign_manifest(run_manifest_path)
-    if signature_path:
-        console.print(f"Run manifest signature: {signature_path}")
 
 
 @presets_app.command("create")
@@ -981,6 +1004,11 @@ def run(
     output_dir: Annotated[Optional[Path], typer.Option(help="Directory to save simulation results")] = None,
     compare_baselines: Annotated[bool, typer.Option(help="Run PID and standard pump baselines in the background")] = True,
     seed: Annotated[Optional[int], typer.Option(help="Random seed for deterministic runs")] = None,
+    patient_model_type: Annotated[str, typer.Option("--patient-model", help="Patient model: auto, bergman, custom, simglucose")] = "auto",
+    sensor_noise_std: Annotated[Optional[float], typer.Option("--sensor-noise-std", help="CGM noise std (mg/dL)")] = None,
+    sensor_lag_minutes: Annotated[Optional[int], typer.Option("--sensor-lag-minutes", help="CGM lag (minutes)")] = None,
+    sensor_dropout_prob: Annotated[Optional[float], typer.Option("--sensor-dropout-prob", help="CGM dropout probability (0-1)")] = None,
+    sensor_bias: Annotated[Optional[float], typer.Option("--sensor-bias", help="CGM bias (mg/dL)")] = None,
     safety_min_glucose: Annotated[Optional[float], typer.Option("--safety-min-glucose", help="Min plausible glucose (mg/dL)")] = None,
     safety_max_glucose: Annotated[Optional[float], typer.Option("--safety-max-glucose", help="Max plausible glucose (mg/dL)")] = None,
     safety_max_glucose_delta_per_5_min: Annotated[Optional[float], typer.Option("--safety-max-glucose-delta-per-5-min", help="Max glucose delta per 5 min (mg/dL)")] = None,
@@ -1060,8 +1088,11 @@ def run(
             validated_patient_params = load_patient_config_by_name(patient_config_name).model_dump()
             patient_label = patient_config_name
 
-        patient_model = iints.PatientModel(**validated_patient_params)
-        console.print(f"Using patient model: {patient_model.__class__.__name__} with config [cyan]{patient_label}[/cyan]")
+        patient_model = iints.PatientFactory.create_patient(patient_type=patient_model_type, **validated_patient_params)
+        console.print(
+            f"Using patient model: {patient_model.__class__.__name__} "
+            f"({patient_model_type}) with config [cyan]{patient_label}[/cyan]"
+        )
     except ValidationError as e:
         console.print("[bold red]Patient config validation failed:[/bold red]")
         for line in format_validation_error(e):
@@ -1125,12 +1156,31 @@ def run(
     output_dir = resolve_output_dir(output_dir, run_id)
 
     effective_safety_config = safety_config or SafetyConfig()
+    sensor_model = None
+    if any(v is not None for v in (sensor_noise_std, sensor_lag_minutes, sensor_dropout_prob, sensor_bias)):
+        sensor_model = iints.SensorModel(
+            noise_std=float(sensor_noise_std or 0.0),
+            lag_minutes=int(sensor_lag_minutes or 0),
+            dropout_prob=float(sensor_dropout_prob or 0.0),
+            bias=float(sensor_bias or 0.0),
+            seed=resolved_seed,
+        )
+    elif patient_model_type == "auto":
+        sensor_model = iints.SensorModel(
+            noise_std=7.0,
+            lag_minutes=10,
+            dropout_prob=0.0,
+            bias=0.0,
+            seed=resolved_seed,
+        )
+
     simulator = iints.Simulator(
         patient_model=patient_model,
         algorithm=algorithm_instance,
         time_step=time_step,
         seed=resolved_seed,
         safety_config=effective_safety_config,
+        sensor_model=sensor_model,
     )
     
     for event in stress_events:

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/core/algorithms/mock_algorithms.py

@@ -95,7 +95,10 @@ class RunawayAIAlgorithm(InsulinAlgorithm):
 
     def predict_insulin(self, data: AlgorithmInput) -> Dict[str, Any]:
         trend = data.glucose_trend_mgdl_min
-        if data.current_glucose <= self.trigger_glucose or (trend is not None and trend < 0):
+        current_glucose = data.current_glucose
+        if current_glucose is None:
+            dose = 0.0
+        elif current_glucose <= self.trigger_glucose or (trend is not None and trend < 0):
             dose = self.max_bolus
         else:
             dose = 0.0

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/core/patient/models.py

@@ -16,6 +16,7 @@ class CustomPatientModel:
     def __init__(self, basal_insulin_rate: float = 0.8, insulin_sensitivity: float = 50.0,
                  carb_factor: float = 10.0, glucose_decay_rate: float = 0.002,
                  initial_glucose: float = 120.0, glucose_absorption_rate: float = 0.03,
+                 basal_glucose_target: Optional[float] = None,
                  insulin_action_duration: float = 300.0, # minutes, e.g., 5 hours
                  insulin_peak_time: float = 75.0, # minutes
                  meal_mismatch_epsilon: float = 1.0, # Factor for meal mismatch
@@ -43,6 +44,7 @@ class CustomPatientModel:
         self.carb_factor = carb_factor
         self.glucose_decay_rate = glucose_decay_rate
         self.glucose_absorption_rate = glucose_absorption_rate
+        self.basal_glucose_target = basal_glucose_target if basal_glucose_target is not None else initial_glucose
         self.insulin_action_duration = insulin_action_duration
         self.insulin_peak_time = insulin_peak_time
         self.meal_mismatch_epsilon = meal_mismatch_epsilon
@@ -182,7 +184,8 @@ class CustomPatientModel:
 
 
         # --- Basal metabolic glucose production/consumption (simplified) ---
-        basal_glucose_change = -self.glucose_decay_rate * self.current_glucose * time_step
+        # Homeostatic drift toward a basal target (prevents runaway decline)
+        basal_glucose_change = -self.glucose_decay_rate * (self.current_glucose - self.basal_glucose_target) * time_step
 
         # --- Dawn phenomenon effect ---
         dawn_effect = 0.0

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/core/patient/patient_factory.py

@@ -2,6 +2,13 @@ import numpy as np
 from typing import Dict, Any, Optional
 from .models import CustomPatientModel
 
+try:
+    from .bergman_model import BergmanPatientModel
+    BERGMAN_AVAILABLE = True
+except Exception:
+    BergmanPatientModel = None  # type: ignore[assignment,misc]
+    BERGMAN_AVAILABLE = False
+
 try:
     from simglucose.simulation.env import T1DSimEnv
     from simglucose.patient.t1dpatient import T1DPatient
@@ -25,10 +32,22 @@ class PatientFactory:
     ]
     
     @staticmethod
-    def create_patient(patient_type='custom', patient_id=None, initial_glucose=120.0, **kwargs):
+    def create_patient(patient_type='auto', patient_id=None, initial_glucose=120.0, **kwargs):
         """Create a patient model based on type."""
+        if patient_type == 'auto':
+            if BERGMAN_AVAILABLE and BergmanPatientModel is not None:
+                return BergmanPatientModel(initial_glucose=initial_glucose, **kwargs)
+            if SIMGLUCOSE_AVAILABLE:
+                patient_name = patient_id or PatientFactory.SIMGLUCOSE_PATIENTS[0]
+                return SimglucosePatientWrapper(patient_name, initial_glucose)
+            return CustomPatientModel(initial_glucose=initial_glucose, **kwargs)
         if patient_type == 'custom':
             return CustomPatientModel(initial_glucose=initial_glucose, **kwargs)
+        elif patient_type == 'bergman':
+            if not BERGMAN_AVAILABLE or BergmanPatientModel is None:
+                print("Warning: Bergman model not available, falling back to custom model")
+                return CustomPatientModel(initial_glucose=initial_glucose, **kwargs)
+            return BergmanPatientModel(initial_glucose=initial_glucose, **kwargs)
         elif patient_type == 'simglucose':
             if not SIMGLUCOSE_AVAILABLE:
                 print("Warning: Simglucose not available, falling back to custom model")

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/core/safety/input_validator.py

@@ -1,4 +1,4 @@
-from typing import Optional
+from typing import Any, Dict, Optional
 
 from iints.core.safety.config import SafetyConfig
 
@@ -33,18 +33,18 @@ class InputValidator:
         self.last_valid_glucose: Optional[float] = None
         self.last_validation_time: Optional[float] = None
 
-    def reset(self):
+    def reset(self) -> None:
         """Resets the state of the validator for a new simulation."""
         self.last_valid_glucose = None
         self.last_validation_time = None
 
-    def get_state(self) -> dict:
+    def get_state(self) -> Dict[str, Any]:
         return {
             "last_valid_glucose": self.last_valid_glucose,
             "last_validation_time": self.last_validation_time,
         }
 
-    def set_state(self, state: dict) -> None:
+    def set_state(self, state: Dict[str, Any]) -> None:
         self.last_valid_glucose = state.get("last_valid_glucose")
         self.last_validation_time = state.get("last_validation_time")
 

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/core/safety/supervisor.py

@@ -1,6 +1,7 @@
 from typing import Optional
 
 from iints.core.safety.config import SafetyConfig
+from iints.core.safety.input_validator import InputValidator
 from iints.core.supervisor import IndependentSupervisor as FullSupervisor
 
 class IndependentSupervisor(FullSupervisor):
@@ -31,9 +32,3 @@ class IndependentSupervisor(FullSupervisor):
 
 # Alias for backward compatibility as the codebase migrates
 SafetySupervisor = IndependentSupervisor
-
-class InputValidator:
-    """
-    Validates simulation inputs.
-    """
-    pass

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/core/simulator.py

@@ -115,9 +115,6 @@ class Simulator:
         self.simulation_data: List[Any] = [] # To store results
         self.stress_events: List[StressEvent] = []
         self.seed = seed
-        if self.seed is not None:
-            np.random.seed(self.seed) # Set numpy seed for reproducibility
-            # Potentially set other seeds here if other random modules are used (e.g., random.seed(self.seed))
         self.safety_config = safety_config or SafetyConfig()
         self.supervisor = IndependentSupervisor(safety_config=self.safety_config)
         self.input_validator = InputValidator(safety_config=self.safety_config)

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/core/supervisor.py

@@ -1,5 +1,5 @@
 import numpy as np
-from typing import Dict, Any, Optional, List, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 
 from iints.core.safety.config import SafetyConfig
 from dataclasses import dataclass
@@ -42,18 +42,18 @@ class IndependentSupervisor:
     Implements hard safety limits and emergency overrides.
     """
     
-    def __init__(self, 
-                 hypoglycemia_threshold=70,      # mg/dL
-                 severe_hypoglycemia_threshold=54,  # mg/dL
-                 hyperglycemia_threshold=250,    # mg/dL
-                 max_insulin_per_bolus=5,        # Units
-                 glucose_rate_alarm=5,           # mg/dL per minute
-                 max_60min=3.0,                  # Units per 60 minutes
-                 max_iob=4.0,                    # Units
-                 trend_stop=-2.0,                # mg/dL per minute
-                 hypo_cutoff=70.0,               # mg/dL
-                 predicted_hypoglycemia_threshold=60.0,  # mg/dL
-                 predicted_hypoglycemia_horizon_minutes=30,  # minutes
+    def __init__(self,
+                 hypoglycemia_threshold: float = 70.0,      # mg/dL
+                 severe_hypoglycemia_threshold: float = 54.0,  # mg/dL
+                 hyperglycemia_threshold: float = 250.0,    # mg/dL
+                 max_insulin_per_bolus: float = 5.0,        # Units
+                 glucose_rate_alarm: float = 5.0,           # mg/dL per minute
+                 max_60min: float = 3.0,                    # Units per 60 minutes
+                 max_iob: float = 4.0,                      # Units
+                 trend_stop: float = -2.0,                  # mg/dL per minute
+                 hypo_cutoff: float = 70.0,                 # mg/dL
+                 predicted_hypoglycemia_threshold: float = 60.0,  # mg/dL
+                 predicted_hypoglycemia_horizon_minutes: int = 30,  # minutes
                  contract_enabled: bool = True,
                  contract_glucose_threshold: float = 90.0,
                  contract_trend_threshold_mgdl_min: float = -1.0,
@@ -95,7 +95,7 @@ class IndependentSupervisor:
         self.violations: List[SafetyViolation] = []
         self.emergency_mode = False
         self.last_iob = 0.0
-        self.dose_history: List[tuple] = []
+        self.dose_history: List[Tuple[float, float]] = []
         
     def evaluate_safety(
         self,
@@ -320,7 +320,7 @@ class IndependentSupervisor:
             ]
         }
     
-    def reset(self):
+    def reset(self) -> None:
         """Reset supervisor state."""
         self.glucose_history.clear()
         self.violations.clear()

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/highlevel.py

@@ -8,9 +8,10 @@ import pandas as pd
 import yaml
 
 from iints.api.base_algorithm import InsulinAlgorithm
-from iints.core.patient.models import PatientModel
+from iints.core.patient.patient_factory import PatientFactory
 from iints.core.patient.profile import PatientProfile
 from iints.core.simulator import Simulator
+from iints.core.devices.models import SensorModel
 from iints.core.safety import SafetyConfig
 from iints.analysis.baseline import run_baseline_comparison, write_baseline_comparison
 from iints.analysis.reporting import ClinicalReportGenerator
@@ -62,6 +63,11 @@ def run_simulation(
     algorithm: Union[InsulinAlgorithm, type],
     scenario: Optional[Union[str, Path, Dict[str, Any]]] = None,
     patient_config: Union[str, Path, Dict[str, Any], PatientProfile] = "default_patient",
+    patient_model_type: str = "auto",
+    sensor_noise_std: Optional[float] = None,
+    sensor_lag_minutes: Optional[int] = None,
+    sensor_dropout_prob: Optional[float] = None,
+    sensor_bias: Optional[float] = None,
     duration_minutes: int = 720,
     time_step: int = 5,
     seed: Optional[int] = None,
@@ -81,12 +87,30 @@ def run_simulation(
     output_path = resolve_output_dir(output_dir, run_id)
 
     patient_params = _resolve_patient_config(patient_config)
-    patient_model = PatientModel(**patient_params)
+    patient_model = PatientFactory.create_patient(patient_type=patient_model_type, **patient_params)
 
     scenario_payload = _resolve_scenario_payloads(scenario)
     stress_event_payloads = scenario_payload.get("stress_events", []) if scenario_payload else []
     effective_safety_config = safety_config or SafetyConfig()
 
+    sensor_model = None
+    if any(v is not None for v in (sensor_noise_std, sensor_lag_minutes, sensor_dropout_prob, sensor_bias)):
+        sensor_model = SensorModel(
+            noise_std=float(sensor_noise_std or 0.0),
+            lag_minutes=int(sensor_lag_minutes or 0),
+            dropout_prob=float(sensor_dropout_prob or 0.0),
+            bias=float(sensor_bias or 0.0),
+            seed=resolved_seed,
+        )
+    elif patient_model_type == "auto":
+        sensor_model = SensorModel(
+            noise_std=7.0,
+            lag_minutes=10,
+            dropout_prob=0.0,
+            bias=0.0,
+            seed=resolved_seed,
+        )
+
     simulator = Simulator(
         patient_model=patient_model,
         algorithm=algorithm_instance,
@@ -94,6 +118,7 @@ def run_simulation(
         seed=resolved_seed,
         safety_config=effective_safety_config,
         predictor=predictor,
+        sensor_model=sensor_model,
     )
     for event in build_stress_events(stress_event_payloads):
         simulator.add_stress_event(event)
@@ -127,6 +152,7 @@ def run_simulation(
             "metadata": algorithm_instance.get_algorithm_metadata().to_dict(),
         },
         "patient_config": patient_params,
+        "patient_model_type": patient_model_type,
         "scenario": scenario_payload,
         "duration_minutes": duration_minutes,
         "time_step_minutes": time_step,
@@ -135,6 +161,7 @@ def run_simulation(
         "export_audit": export_audit,
         "generate_report": generate_report,
         "safety_config": asdict(effective_safety_config),
+        "sensor_model": sensor_model.get_state() if sensor_model else None,
     }
     config_path = output_path / "config.json"
     write_json(config_path, config_payload)
@@ -202,6 +229,11 @@ def run_full(
     algorithm: Union[InsulinAlgorithm, type],
     scenario: Optional[Union[str, Path, Dict[str, Any]]] = None,
     patient_config: Union[str, Path, Dict[str, Any], PatientProfile] = "default_patient",
+    patient_model_type: str = "auto",
+    sensor_noise_std: Optional[float] = None,
+    sensor_lag_minutes: Optional[int] = None,
+    sensor_dropout_prob: Optional[float] = None,
+    sensor_bias: Optional[float] = None,
     duration_minutes: int = 720,
     time_step: int = 5,
     seed: Optional[int] = None,
@@ -219,12 +251,30 @@ def run_full(
     output_path = resolve_output_dir(output_dir, run_id)
 
     patient_params = _resolve_patient_config(patient_config)
-    patient_model = PatientModel(**patient_params)
+    patient_model = PatientFactory.create_patient(patient_type=patient_model_type, **patient_params)
 
     scenario_payload = _resolve_scenario_payloads(scenario)
     stress_event_payloads = scenario_payload.get("stress_events", []) if scenario_payload else []
     effective_safety_config = safety_config or SafetyConfig()
 
+    sensor_model = None
+    if any(v is not None for v in (sensor_noise_std, sensor_lag_minutes, sensor_dropout_prob, sensor_bias)):
+        sensor_model = SensorModel(
+            noise_std=float(sensor_noise_std or 0.0),
+            lag_minutes=int(sensor_lag_minutes or 0),
+            dropout_prob=float(sensor_dropout_prob or 0.0),
+            bias=float(sensor_bias or 0.0),
+            seed=resolved_seed,
+        )
+    elif patient_model_type == "auto":
+        sensor_model = SensorModel(
+            noise_std=7.0,
+            lag_minutes=10,
+            dropout_prob=0.0,
+            bias=0.0,
+            seed=resolved_seed,
+        )
+
     simulator = Simulator(
         patient_model=patient_model,
         algorithm=algorithm_instance,
@@ -233,6 +283,7 @@ def run_full(
         enable_profiling=enable_profiling,
         safety_config=effective_safety_config,
         predictor=predictor,
+        sensor_model=sensor_model,
     )
     for event in build_stress_events(stress_event_payloads):
         simulator.add_stress_event(event)
@@ -274,6 +325,7 @@ def run_full(
         "generate_report": True,
         "enable_profiling": enable_profiling,
         "safety_config": asdict(effective_safety_config),
+        "sensor_model": sensor_model.get_state() if sensor_model else None,
     }
     config_path = output_path / "config.json"
     write_json(config_path, config_payload)
@@ -345,7 +397,7 @@ def run_population(
     max_workers: Optional[int] = None,
     safety_config: Optional[SafetyConfig] = None,
     safety_weights: Optional[Dict[str, float]] = None,
-    patient_model_type: str = "custom",
+    patient_model_type: str = "auto",
     population_cv: Optional[Dict[str, float]] = None,
 ) -> Dict[str, Any]:
     """

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/research/__init__.py

@@ -7,9 +7,11 @@ from .dataset import (
     save_parquet,
     load_dataset,
     save_dataset,
+    compute_dataset_lineage,
 )
 from .predictor import LSTMPredictor, load_predictor, PredictorService, load_predictor_service
-from .losses import QuantileLoss, SafetyWeightedMSE
+from .losses import QuantileLoss, SafetyWeightedMSE, BandWeightedMSE
+from .metrics import regression_metrics, band_regression_metrics, interval_coverage_metrics
 
 __all__ = [
     "PredictorConfig",
@@ -21,10 +23,15 @@ __all__ = [
     "save_parquet",
     "load_dataset",
     "save_dataset",
+    "compute_dataset_lineage",
     "LSTMPredictor",
     "load_predictor",
     "PredictorService",
     "load_predictor_service",
     "QuantileLoss",
     "SafetyWeightedMSE",
+    "BandWeightedMSE",
+    "regression_metrics",
+    "band_regression_metrics",
+    "interval_coverage_metrics",
 ]

{iints_sdk_python35-0.1.18 → iints_sdk_python35-0.1.20}/src/iints/research/config.py

@@ -52,7 +52,7 @@ class TrainingConfig:
     # P3-10: Normalization strategy.  Options: "zscore", "robust", "none".
     normalization: str = "zscore"
 
-    # P3-12: Loss function.  Options: "mse", "quantile".
+    # P3-12: Loss function.  Options: "mse", "quantile", "safety_weighted", "band_weighted".
     # For quantile loss, also set `quantile` (0 < q < 1).
     loss: str = "mse"
     quantile: Optional[float] = None  # e.g. 0.9 for 90th-percentile upper bound
@@ -66,3 +66,17 @@ class TrainingConfig:
     safety_weighted_low_threshold: float = 80.0
     safety_weighted_alpha: float = 2.0
     safety_weighted_max_weight: float = 4.0
+
+    # Band-weighted loss (penalize low/high glucose errors)
+    band_weighted_low_threshold: float = 70.0
+    band_weighted_high_threshold: float = 180.0
+    band_weighted_low_weight: float = 2.0
+    band_weighted_high_weight: float = 1.5
+    band_weighted_max_weight: float = 5.0
+
+    # Optional: pre-announced meals (clinically common for AID systems).
+    # If enabled, create `meal_announcement_feature` by shifting
+    # `meal_announcement_column` earlier by `meal_announcement_minutes`.
+    meal_announcement_minutes: Optional[float] = None
+    meal_announcement_column: str = "carb_intake_grams"
+    meal_announcement_feature: str = "meal_announcement_grams"