psdl-lang 0.2.0__tar.gz

psdl_lang-0.2.0/LICENSE

@@ -0,0 +1,190 @@
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psdl_lang-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: psdl-lang
+Version: 0.2.0
+Summary: Patient Scenario Definition Language - Reference Implementation
+Author-email: Ziyuan Guan <ziyuan.guan@ufl.edu>
+Maintainer-email: Ziyuan Guan <ziyuan.guan@ufl.edu>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/Chesterguan/PSDL
+Project-URL: Documentation, https://github.com/Chesterguan/PSDL#readme
+Project-URL: Repository, https://github.com/Chesterguan/PSDL
+Project-URL: Issues, https://github.com/Chesterguan/PSDL/issues
+Project-URL: Changelog, https://github.com/Chesterguan/PSDL/blob/main/CHANGELOG.md
+Keywords: healthcare,clinical,patient,scenario,DSL,OMOP,FHIR,EHR,temporal,medical
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pyyaml>=6.0
+Provides-Extra: full
+Requires-Dist: requests>=2.28; extra == "full"
+Requires-Dist: sqlalchemy>=2.0; extra == "full"
+Provides-Extra: omop
+Requires-Dist: sqlalchemy>=2.0; extra == "omop"
+Provides-Extra: fhir
+Requires-Dist: requests>=2.28; extra == "fhir"
+Provides-Extra: streaming
+Requires-Dist: apache-flink>=1.17; extra == "streaming"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: jsonschema>=4.0; extra == "dev"
+Requires-Dist: lark>=1.1; extra == "dev"
+Requires-Dist: black>=23.0; extra == "dev"
+Requires-Dist: isort>=5.12; extra == "dev"
+Requires-Dist: mypy>=1.0; extra == "dev"
+Requires-Dist: requests>=2.28; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=6.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.3; extra == "docs"
+Requires-Dist: myst-parser>=2.0; extra == "docs"
+Provides-Extra: notebook
+Requires-Dist: jupyter>=1.0; extra == "notebook"
+Requires-Dist: ipywidgets>=8.0; extra == "notebook"
+Requires-Dist: pandas>=2.0; extra == "notebook"
+Requires-Dist: matplotlib>=3.7; extra == "notebook"
+Provides-Extra: all
+Requires-Dist: psdl-lang[dev,docs,full,notebook,streaming]; extra == "all"
+Dynamic: license-file
+
+<p align="center">
+  <img src="docs/assets/logo.jpeg" alt="PSDL Logo" width="400"/>
+</p>
+
+<h1 align="center">PSDL</h1>
+<h3 align="center">Patient Scenario Definition Language</h3>
+
+<p align="center">
+  <em>An Open Standard for Clinical Logic, Real-Time Monitoring & AI Integration</em>
+</p>
+
+<p align="center">
+  <a href="https://github.com/Chesterguan/PSDL/actions/workflows/ci.yml"><img src="https://github.com/Chesterguan/PSDL/actions/workflows/ci.yml/badge.svg" alt="Tests"></a>
+  <a href="#specification"><img src="https://img.shields.io/badge/Spec-0.1.0-blue?style=flat-square" alt="Spec Version"></a>
+  <a href="#license"><img src="https://img.shields.io/badge/License-Apache%202.0-green?style=flat-square" alt="License"></a>
+  <a href="#contributing"><img src="https://img.shields.io/badge/PRs-Welcome-brightgreen?style=flat-square" alt="PRs Welcome"></a>
+  <img src="https://img.shields.io/badge/Python-3.8%20%7C%203.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue?style=flat-square&logo=python&logoColor=white" alt="Python 3.8-3.12">
+</p>
+
+<p align="center">
+  <strong>What SQL became for data queries, ONNX for ML models, and GraphQL for APIs —<br/>
+  PSDL is becoming the <em>semantic layer</em> for clinical AI.</strong>
+</p>
+
+<p align="center">
+  📄 <strong>Read the Whitepaper:</strong>
+  <a href="docs/WHITEPAPER_EN.md">English</a> ·
+  <a href="docs/WHITEPAPER_ZH.md">简体中文</a> ·
+  <a href="docs/WHITEPAPER_ES.md">Español</a> ·
+  <a href="docs/WHITEPAPER_FR.md">Français</a> ·
+  <a href="docs/WHITEPAPER_JA.md">日本語</a>
+</p>
+
+---
+
+## Try It Now (No Setup Required)
+
+Run PSDL in your browser with Google Colab - zero installation, real clinical data:
+
+| Notebook | Data | Description |
+|----------|------|-------------|
+| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Chesterguan/PSDL/blob/main/notebooks/PSDL_Colab_Synthea.ipynb) | **Synthetic** | Quick demo with generated patient data (2 min) |
+| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Chesterguan/PSDL/blob/main/notebooks/PSDL_Colab_MIMIC_Demo.ipynb) | **MIMIC-IV Demo** | 100 real ICU patients, ICD diagnoses |
+| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Chesterguan/PSDL/blob/main/notebooks/PSDL_Colab_Sepsis_Challenge.ipynb) | **PhysioNet Sepsis** | 40,000+ patients with labeled sepsis |
+
+---
+
+## The Problem
+
+Despite significant advances in clinical AI and machine learning, **real-time decision support in healthcare remains fragmented, non-portable, non-reproducible, and exceptionally difficult to audit or regulate**.
+
+<p align="center">
+  <img src="docs/assets/layers.jpeg" alt="Healthcare AI Semantic Stack" width="800"/>
+  <br/>
+  <em>PSDL fills the missing semantic layer in the healthcare AI stack</em>
+</p>
+
+## What is PSDL?
+
+PSDL (Patient Scenario Definition Language) is a declarative, vendor-neutral language for expressing clinical scenarios. It provides a structured way to define:
+
+| Component | Description |
+|-----------|-------------|
+| **Signals** | Time-series clinical data bindings (labs, vitals, etc.) |
+| **Trends** | Temporal computations over signals (deltas, slopes, averages) |
+| **Logic** | Boolean algebra combining trends into clinical states |
+| **Population** | Criteria for which patients a scenario applies to |
+| **Triggers** | Event-condition-action rules (v0.2) |
+
+<p align="center">
+  <img src="docs/assets/semantic langauge.jpeg" alt="How PSDL Works" width="800"/>
+  <br/>
+  <em>Syntax vs Semantics vs Runtime - How PSDL Works</em>
+</p>
+
+## Quick Example
+
+```yaml
+# Detect early kidney injury
+scenario: AKI_Early_Detection
+version: "0.1.0"
+
+signals:
+  Cr:
+    source: creatinine
+    concept_id: 3016723  # OMOP concept
+    unit: mg/dL
+
+trends:
+  cr_rising:
+    expr: delta(Cr, 6h) > 0.3
+    description: "Creatinine rise > 0.3 mg/dL in 6 hours"
+
+  cr_high:
+    expr: last(Cr) > 1.5
+    description: "Current creatinine elevated"
+
+logic:
+  aki_risk:
+    expr: cr_rising AND cr_high
+    severity: high
+    description: "Early AKI - rising and elevated creatinine"
+```
+
+## Why PSDL?
+
+| Challenge | Without PSDL | With PSDL |
+|-----------|--------------|-----------|
+| **Portability** | Logic tied to specific hospital systems | Same scenario runs anywhere with mapping |
+| **Auditability** | Scattered across Python, SQL, configs | Single structured, version-controlled file |
+| **Reproducibility** | Hidden state, implicit dependencies | Deterministic execution, explicit semantics |
+| **Regulatory Compliance** | Manual documentation | Built-in audit primitives |
+| **Research Sharing** | Cannot validate published scenarios | Portable, executable definitions |
+
+## Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/Chesterguan/PSDL.git
+cd psdl
+
+# Install dependencies
+pip install -r requirements.txt
+```
+
+## Usage
+
+### Parse a Scenario
+
+```python
+from psdl import PSDLParser
+
+parser = PSDLParser()
+scenario = parser.parse_file("examples/aki_detection.yaml")
+
+print(f"Scenario: {scenario.name}")
+print(f"Signals: {list(scenario.signals.keys())}")
+print(f"Logic rules: {list(scenario.logic.keys())}")
+```
+
+### Evaluate Against Patient Data
+
+```python
+from psdl import PSDLParser, PSDLEvaluator, InMemoryBackend
+from psdl.operators import DataPoint
+from datetime import datetime, timedelta
+
+# Parse scenario
+parser = PSDLParser()
+scenario = parser.parse_file("examples/aki_detection.yaml")
+
+# Set up data backend
+backend = InMemoryBackend()
+now = datetime.now()
+
+# Add patient data
+backend.add_data(
+    patient_id=123,
+    signal_name="Cr",
+    data=[
+        DataPoint(now - timedelta(hours=6), 1.0),
+        DataPoint(now - timedelta(hours=3), 1.3),
+        DataPoint(now, 1.8),
+    ]
+)
+
+# Evaluate
+evaluator = PSDLEvaluator(scenario, backend)
+result = evaluator.evaluate_patient(patient_id=123, reference_time=now)
+
+if result.is_triggered:
+    print(f"Patient triggered: {result.triggered_logic}")
+    print(f"Trend values: {result.trend_values}")
+```
+
+## Temporal Operators
+
+| Operator | Syntax | Description |
+|----------|--------|-------------|
+| `delta` | `delta(signal, window)` | Absolute change over window |
+| `slope` | `slope(signal, window)` | Linear regression slope |
+| `ema` | `ema(signal, window)` | Exponential moving average |
+| `sma` | `sma(signal, window)` | Simple moving average |
+| `min` | `min(signal, window)` | Minimum value in window |
+| `max` | `max(signal, window)` | Maximum value in window |
+| `count` | `count(signal, window)` | Observation count |
+| `last` | `last(signal)` | Most recent value |
+
+### Window Formats
+
+- `30s` - 30 seconds
+- `5m` - 5 minutes
+- `6h` - 6 hours
+- `1d` - 1 day
+- `7d` - 7 days
+
+## Project Structure
+
+PSDL follows industry-standard patterns (like GraphQL, CQL, ONNX): 
+ - **Specification** defines WHAT
+ - **Reference Implementation** shows HOW.
+
+```
+psdl/
+├── README.md              # This file
+├── spec/                  # SPECIFICATION
+│   └── schema-v0.1.yaml   # YAML schema + operator semantics
+├── src/psdl/              # REFERENCE IMPLEMENTATION (Python)
+│   ├── __init__.py
+│   ├── parser.py          # YAML parser
+│   ├── evaluator.py       # Batch execution mode
+│   ├── operators.py       # Temporal operators
+│   ├── execution/         # Execution Modes
+│   │   ├── batch.py       # Batch mode + SQL compiler
+│   │   └── streaming/     # Streaming mode (Flink)
+│   └── adapters/          # Data Adapters
+│       ├── omop.py        # OMOP CDM adapter (SQL)
+│       └── fhir.py        # FHIR R4 adapter (REST)
+├── examples/              # Example scenarios
+│   ├── icu_deterioration.yaml
+│   ├── aki_detection.yaml
+│   └── sepsis_screening.yaml
+├── docs/
+│   ├── getting-started.md
+│   ├── WHITEPAPER.md      # Full specification document
+│   └── assets/            # Images and diagrams
+└── tests/
+    ├── test_parser.py
+    └── test_evaluator.py
+```
+
+| Component | Description |
+|-----------|-------------|
+| **Specification** | PSDL language definition (YAML schema + operator semantics) |
+| **Reference Implementation** | Python implementation demonstrating the spec |
+| **Parser** | Parses PSDL YAML into internal representation |
+| **Evaluator** | Executes parsed scenarios (batch mode) |
+| **Data Adapter** | Interface to clinical data sources (OMOP, FHIR) |
+
+## Running Tests
+
+```bash
+# Run all tests
+pytest tests/ -v
+
+# Run with verbose output
+pytest tests/ -v -s
+```
+
+### Test Coverage: 234 Tests (All Passing)
+
+- **Unit Tests**: Parser, evaluator, operators, scenarios
+- **Integration Tests**: FHIR adapter, OMOP backend with population filtering
+- **Validation**: SQL equivalence (100% match), KDIGO clinical guidelines
+- **Streaming Tests**: Window functions, logic evaluation, Flink compiler
+
+See [tests/TEST_VALIDATION.md](tests/TEST_VALIDATION.md) for detailed methodology.
+
+## Example Scenarios
+
+| Scenario | Description | Clinical Use |
+|----------|-------------|--------------|
+| **ICU Deterioration** | Monitors for early signs of clinical deterioration | Kidney function, lactate trends, hemodynamics |
+| **AKI Detection** | KDIGO criteria for Acute Kidney Injury staging | Creatinine-based staging |
+| **Sepsis Screening** | qSOFA + lactate-based sepsis screening | Early sepsis identification |
+
+## Design Principles
+
+| Principle | Description |
+|-----------|-------------|
+| **Declarative** | Define *what* to detect, not *how* to compute it |
+| **Portable** | Same scenario runs on any OMOP/FHIR backend with mapping |
+| **Auditable** | Structured format enables static analysis and version control |
+| **Deterministic** | Predictable execution with no hidden state |
+| **Open** | Vendor-neutral, community-governed |
+
+## Roadmap
+
+| Phase | Status | Focus |
+|-------|--------|-------|
+| **Phase 1: Semantic Foundation** | ✅ Complete | Spec, parser, operators, OMOP/FHIR adapters, 234 tests |
+| **Phase 2: Enhanced Runtime** | 🚧 Current | ✅ Streaming, ✅ SQL generation, triggers, packaging |
+| **Phase 3: Community** | 📋 Planned | Blog series, conferences, tooling ecosystem |
+| **Phase 4: Adoption** | 🔮 Future | Hospital pilots, standards engagement |
+
+📍 **[View Full Roadmap →](docs/ROADMAP.md)**
+
+## Related Standards
+
+| Standard | Relationship |
+|----------|--------------|
+| **OMOP CDM** | Data model for signals (concept_id references) |
+| **FHIR** | Planned runtime target |
+| **CQL** | Similar domain, different scope (quality measures) |
+| **ONNX** | Inspiration for portable format approach |
+
+## Documentation
+
+| Document | Description |
+|----------|-------------|
+| [Whitepaper](docs/WHITEPAPER.md) | Full project vision and specification (5 languages) |
+| [Getting Started](docs/getting-started.md) | Quick start guide |
+| [Roadmap](docs/ROADMAP.md) | Development phases and timeline |
+| [Schema](spec/schema-v0.1.yaml) | YAML schema definition |
+| [Changelog](CHANGELOG.md) | Version history |
+
+## Contributing
+
+We welcome contributions! See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+### Ways to Contribute
+
+- **Specification**: Propose language features, operators, semantics
+- **Implementation**: Build runtimes, backends, tooling
+- **Documentation**: Improve guides, tutorials, examples
+- **Testing**: Add conformance tests, find edge cases
+- **Adoption**: Share use cases, pilot experiences
+
+## License
+
+Apache 2.0 - See [LICENSE](LICENSE) for details.
+
+---
+
+<p align="center">
+  <strong>Clinical AI doesn't fail because models are weak.<br/>
+  It fails because there's no semantic layer to express clinical logic portably.</strong>
+</p>
+
+<p align="center">
+  <em>PSDL is the semantic layer for clinical AI — like SQL for databases.</em>
+</p>
+
+<p align="center">
+  <sub>An open standard built by the community, for the community.</sub>
+</p>