@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

package/bin/skills/pyhealth/references/tasks.md

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+# PyHealth Clinical Prediction Tasks
+
+## Overview
+
+PyHealth provides 20+ predefined clinical prediction tasks for common healthcare AI applications. Each task function transforms raw patient data into structured input-output pairs for model training.
+
+## Task Function Structure
+
+All task functions inherit from `BaseTask` and provide:
+
+- **input_schema**: Defines input features (diagnoses, medications, labs, etc.)
+- **output_schema**: Defines prediction targets (labels, values)
+- **pre_filter()**: Optional patient/visit filtering logic
+
+**Usage Pattern:**
+```python
+from pyhealth.datasets import MIMIC4Dataset
+from pyhealth.tasks import mortality_prediction_mimic4_fn
+
+dataset = MIMIC4Dataset(root="/path/to/data")
+sample_dataset = dataset.set_task(mortality_prediction_mimic4_fn)
+```
+
+## Electronic Health Record (EHR) Tasks
+
+### Mortality Prediction
+
+**Purpose:** Predict patient death risk at next visit or within specified timeframe
+
+**MIMIC-III Mortality** (`mortality_prediction_mimic3_fn`)
+- Predicts death at next hospital visit
+- Binary classification task
+- Input: Historical diagnoses, procedures, medications
+- Output: Binary label (deceased/alive)
+
+**MIMIC-IV Mortality** (`mortality_prediction_mimic4_fn`)
+- Updated version for MIMIC-IV dataset
+- Enhanced feature set
+- Improved label quality
+
+**eICU Mortality** (`mortality_prediction_eicu_fn`)
+- Multi-center ICU mortality prediction
+- Accounts for hospital-level variation
+
+**OMOP Mortality** (`mortality_prediction_omop_fn`)
+- Standardized mortality prediction
+- Works with OMOP common data model
+
+**In-Hospital Mortality** (`inhospital_mortality_prediction_mimic4_fn`)
+- Predicts death during current hospitalization
+- Real-time risk assessment
+- Earlier prediction window than next-visit mortality
+
+**StageNet Mortality** (`mortality_prediction_mimic4_fn_stagenet`)
+- Specialized for StageNet model architecture
+- Temporal stage-aware prediction
+
+### Hospital Readmission Prediction
+
+**Purpose:** Identify patients at risk of hospital readmission within specified timeframe (typically 30 days)
+
+**MIMIC-III Readmission** (`readmission_prediction_mimic3_fn`)
+- 30-day readmission prediction
+- Binary classification
+- Input: Diagnosis history, medications, demographics
+- Output: Binary label (readmitted/not readmitted)
+
+**MIMIC-IV Readmission** (`readmission_prediction_mimic4_fn`)
+- Enhanced readmission features
+- Improved temporal modeling
+
+**eICU Readmission** (`readmission_prediction_eicu_fn`)
+- ICU-specific readmission risk
+- Multi-site data
+
+**OMOP Readmission** (`readmission_prediction_omop_fn`)
+- Standardized readmission prediction
+
+### Length of Stay Prediction
+
+**Purpose:** Estimate hospital stay duration for resource planning and patient management
+
+**MIMIC-III Length of Stay** (`length_of_stay_prediction_mimic3_fn`)
+- Regression task
+- Input: Admission diagnoses, vitals, demographics
+- Output: Continuous value (days)
+
+**MIMIC-IV Length of Stay** (`length_of_stay_prediction_mimic4_fn`)
+- Enhanced features for LOS prediction
+- Better temporal granularity
+
+**eICU Length of Stay** (`length_of_stay_prediction_eicu_fn`)
+- ICU stay duration prediction
+- Multi-hospital data
+
+**OMOP Length of Stay** (`length_of_stay_prediction_omop_fn`)
+- Standardized LOS prediction
+
+### Drug Recommendation
+
+**Purpose:** Suggest appropriate medications based on patient history and current conditions
+
+**MIMIC-III Drug Recommendation** (`drug_recommendation_mimic3_fn`)
+- Multi-label classification
+- Input: Diagnoses, previous medications, demographics
+- Output: Set of recommended drug codes
+- Considers drug-drug interactions
+
+**MIMIC-IV Drug Recommendation** (`drug_recommendation_mimic4_fn`)
+- Updated medication data
+- Enhanced interaction modeling
+
+**eICU Drug Recommendation** (`drug_recommendation_eicu_fn`)
+- Critical care medication recommendations
+
+**OMOP Drug Recommendation** (`drug_recommendation_omop_fn`)
+- Standardized drug recommendation
+
+**Key Considerations:**
+- Handles polypharmacy scenarios
+- Multi-label prediction (multiple drugs per patient)
+- Can integrate with SafeDrug/GAMENet models for safety-aware recommendations
+
+## Specialized Clinical Tasks
+
+### Medical Coding
+
+**MIMIC-III ICD-9 Coding** (`icd9_coding_mimic3_fn`)
+- Assigns ICD-9 diagnosis/procedure codes to clinical notes
+- Multi-label text classification
+- Input: Clinical text/documentation
+- Output: Set of ICD-9 codes
+- Supports both diagnosis and procedure coding
+
+### Patient Linkage
+
+**MIMIC-III Patient Linking** (`patient_linkage_mimic3_fn`)
+- Record matching and deduplication
+- Binary classification (same patient or not)
+- Input: Demographic and clinical features from two records
+- Output: Match probability
+
+## Physiological Signal Tasks
+
+### Sleep Staging
+
+**Purpose:** Classify sleep stages from EEG/physiological signals for sleep disorder diagnosis
+
+**ISRUC Sleep Staging** (`sleep_staging_isruc_fn`)
+- Multi-class classification (Wake, N1, N2, N3, REM)
+- Input: Multi-channel EEG signals
+- Output: Sleep stage per epoch (typically 30 seconds)
+
+**SleepEDF Sleep Staging** (`sleep_staging_sleepedf_fn`)
+- Standard sleep staging task
+- PSG signal processing
+
+**SHHS Sleep Staging** (`sleep_staging_shhs_fn`)
+- Large-scale sleep study data
+- Population-level sleep analysis
+
+**Standardized Labels:**
+- Wake (W)
+- Non-REM Stage 1 (N1)
+- Non-REM Stage 2 (N2)
+- Non-REM Stage 3 (N3/Deep Sleep)
+- REM (Rapid Eye Movement)
+
+### EEG Analysis
+
+**Abnormality Detection** (`abnormality_detection_tuab_fn`)
+- Binary classification (normal/abnormal EEG)
+- Clinical screening application
+- Input: Multi-channel EEG recordings
+- Output: Binary label
+
+**Event Detection** (`event_detection_tuev_fn`)
+- Identify specific EEG events (spikes, seizures)
+- Multi-class classification
+- Input: EEG time series
+- Output: Event type and timing
+
+**Seizure Detection** (`seizure_detection_tusz_fn`)
+- Specialized epileptic seizure detection
+- Critical for epilepsy monitoring
+- Input: Continuous EEG
+- Output: Seizure/non-seizure classification
+
+## Medical Imaging Tasks
+
+### COVID-19 Chest X-ray Classification
+
+**COVID-19 CXR** (`covid_classification_cxr_fn`)
+- Multi-class image classification
+- Classes: COVID-19, bacterial pneumonia, viral pneumonia, normal
+- Input: Chest X-ray images
+- Output: Disease classification
+
+## Text-Based Tasks
+
+### Medical Transcription Classification
+
+**Medical Specialty Classification** (`medical_transcription_classification_fn`)
+- Classify clinical notes by medical specialty
+- Multi-class text classification
+- Input: Clinical transcription text
+- Output: Medical specialty (Cardiology, Neurology, etc.)
+
+## Custom Task Creation
+
+### Creating Custom Tasks
+
+Define custom prediction tasks by specifying input/output schemas:
+
+```python
+from pyhealth.tasks import BaseTask
+
+def custom_task_fn(patient):
+    """Custom prediction task"""
+
+    # Define input features
+    samples = []
+
+    for i, visit in enumerate(patient.visits):
+        # Skip if not enough history
+        if i < 2:
+            continue
+
+        # Create input from historical visits
+        input_info = {
+            "diagnoses": [],
+            "medications": [],
+            "procedures": []
+        }
+
+        # Collect features from previous visits
+        for past_visit in patient.visits[:i]:
+            for event in past_visit.events:
+                if event.vocabulary == "ICD10CM":
+                    input_info["diagnoses"].append(event.code)
+                elif event.vocabulary == "NDC":
+                    input_info["medications"].append(event.code)
+
+        # Define prediction target
+        # Example: predict specific outcome at current visit
+        output_info = {
+            "label": 1 if some_condition else 0
+        }
+
+        samples.append({
+            "patient_id": patient.patient_id,
+            "visit_id": visit.visit_id,
+            "input_info": input_info,
+            "output_info": output_info
+        })
+
+    return samples
+
+# Apply custom task
+sample_dataset = dataset.set_task(custom_task_fn)
+```
+
+### Task Function Components
+
+1. **Input Schema Definition**
+   - Specify which features to extract
+   - Define feature types (codes, sequences, values)
+   - Set temporal windows
+
+2. **Output Schema Definition**
+   - Define prediction targets
+   - Set label types (binary, multi-class, multi-label, regression)
+   - Specify evaluation metrics
+
+3. **Filtering Logic**
+   - Exclude patients/visits with insufficient data
+   - Apply inclusion/exclusion criteria
+   - Handle missing data
+
+4. **Sample Generation**
+   - Create input-output pairs
+   - Maintain patient/visit identifiers
+   - Preserve temporal ordering
+
+## Task Selection Guidelines
+
+### Clinical Prediction Tasks
+**Use when:** Working with structured EHR data (diagnoses, medications, procedures)
+
+**Datasets:** MIMIC-III, MIMIC-IV, eICU, OMOP
+
+**Common tasks:**
+- Mortality prediction for risk stratification
+- Readmission prediction for care transition planning
+- Length of stay for resource allocation
+- Drug recommendation for clinical decision support
+
+### Signal Processing Tasks
+**Use when:** Working with physiological time-series data
+
+**Datasets:** SleepEDF, SHHS, ISRUC, TUEV, TUAB, TUSZ
+
+**Common tasks:**
+- Sleep staging for sleep disorder diagnosis
+- EEG abnormality detection for screening
+- Seizure detection for epilepsy monitoring
+
+### Imaging Tasks
+**Use when:** Working with medical images
+
+**Datasets:** COVID-19 CXR
+
+**Common tasks:**
+- Disease classification from radiographs
+- Abnormality detection
+
+### Text Tasks
+**Use when:** Working with clinical notes and documentation
+
+**Datasets:** Medical Transcriptions, MIMIC-III (with notes)
+
+**Common tasks:**
+- Medical coding from clinical text
+- Specialty classification
+- Clinical information extraction
+
+## Task Output Structure
+
+All task functions return `SampleDataset` with:
+
+```python
+sample = {
+    "patient_id": "unique_patient_id",
+    "visit_id": "unique_visit_id",  # if applicable
+    "input_info": {
+        # Input features (diagnoses, medications, etc.)
+    },
+    "output_info": {
+        # Prediction targets (labels, values)
+    }
+}
+```
+
+## Integration with Models
+
+Tasks define the input/output contract for models:
+
+```python
+from pyhealth.datasets import MIMIC4Dataset
+from pyhealth.tasks import mortality_prediction_mimic4_fn
+from pyhealth.models import Transformer
+
+# 1. Create task-specific dataset
+dataset = MIMIC4Dataset(root="/path/to/data")
+sample_dataset = dataset.set_task(mortality_prediction_mimic4_fn)
+
+# 2. Model automatically adapts to task schema
+model = Transformer(
+    dataset=sample_dataset,
+    feature_keys=["diagnoses", "medications"],
+    mode="binary",  # matches task output
+)
+```
+
+## Best Practices
+
+1. **Match task to clinical question**: Choose predefined tasks when available for standardized benchmarking
+
+2. **Consider temporal windows**: Ensure sufficient history for meaningful predictions
+
+3. **Handle class imbalance**: Many clinical outcomes are rare (mortality, readmission)
+
+4. **Validate clinical relevance**: Ensure prediction windows align with clinical decision-making timelines
+
+5. **Use appropriate metrics**: Different tasks require different evaluation metrics (AUROC for binary, macro-F1 for multi-class)
+
+6. **Document exclusion criteria**: Track which patients/visits are filtered and why
+
+7. **Preserve patient privacy**: Always use de-identified data and follow HIPAA/GDPR guidelines