inclusion-criteria-gen

Source: https://github.com/aipoch/medical-research-skills

Inclusion Criteria Generator

Generate and optimize clinical trial subject inclusion/exclusion criteria to balance scientific rigor with recruitment feasibility.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py generate --help

When to Use

• Use this skill when the task is to Generate and optimize clinical trial subject inclusion/exclusion criteria to balance scientific rigor with recruitment feasibility.
• Use this skill for protocol design tasks that require explicit assumptions, bounded scope, and a reproducible output format.
• Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Use Cases

• Protocol Design: Create initial eligibility criteria for new clinical trials
• Criteria Optimization: Refine existing criteria to improve enrollment without compromising safety/efficacy
• Competitive Analysis: Analyze eligibility patterns across similar trials
• Recruitment Strategy: Identify and mitigate barriers to enrollment
• Feasibility Assessment: Evaluate if proposed criteria are realistic for target population

Usage

CLI Usage

# Generate criteria from study design
python scripts/main.py generate \
  --indication "Type 2 Diabetes" \
  --phase "Phase 2" \
  --population "adults" \
  --duration "24 weeks" \
  --output criteria.json

# Optimize existing criteria
python scripts/main.py optimize \
  --input current_criteria.json \
  --enrollment-target 200 \
  --current-enrollment 120 \
  --output optimized_criteria.json

# Analyze criteria complexity
python scripts/main.py analyze \
  --input criteria.json \
  --output analysis_report.json

# Compare with competitor trials
python scripts/main.py benchmark \
  --input criteria.json \
  --condition "Type 2 Diabetes" \
  --output benchmark_report.json

Python API

from scripts.main import CriteriaGenerator, CriteriaOptimizer

# Generate new criteria
generator = CriteriaGenerator()
criteria = generator.generate(
    indication="Type 2 Diabetes",
    phase="Phase 2",
    population="adults",
    study_duration="24 weeks",
    endpoints=["HbA1c reduction", "weight change"]
)

# Optimize existing criteria
optimizer = CriteriaOptimizer()
optimized = optimizer.optimize(
    criteria=existing_criteria,
    enrollment_target=200,
    current_enrollment=120,
    retention_rate=0.85
)

# Analyze criteria complexity
analysis = optimizer.analyze_complexity(criteria)

Input Format

Study Design Parameters

{
  "indication": "Type 2 Diabetes Mellitus",
  "phase": "Phase 2",
  "population": "adults",
  "age_range": {"min": 18, "max": 75},
  "study_duration": "24 weeks",
  "treatment_type": "oral",
  "primary_endpoints": ["HbA1c change from baseline"],
  "safety_considerations": ["cardiovascular risk"],
  "concomitant_meds_allowed": ["metformin"]
}

Existing Criteria Format

{
  "inclusion_criteria": [
    {
      "id": "I1",
      "criterion": "Age 18-75 years",
      "rationale": "Adult population per regulatory guidance",
      "category": "demographics"
    }
  ],
  "exclusion_criteria": [
    {
      "id": "E1",
      "criterion": "HbA1c < 7.0% or > 11.0%",
      "rationale": "Ensure measurable treatment effect",
      "category": "disease_severity"
    }
  ]
}

Output Format

Generated/Optimized Criteria

{
  "inclusion_criteria": [
    {
      "id": "I1",
      "criterion": "Age 18-75 years, inclusive",
      "category": "demographics",
      "rationale": "Adult population; upper limit for safety",
      "priority": "required",
      "impact": "low"
    }
  ],
  "exclusion_criteria": [
    {
      "id": "E1",
      "criterion": "HbA1c < 7.5% or > 10.5% at screening",
      "category": "disease_severity",
      "rationale": "Optimal range for detecting treatment effect",
      "priority": "required",
      "impact": "medium",
      "flexibility": "widen by 0.5% if enrollment slow"
    }
  ],
  "optimization_notes": [
    "Widened HbA1c range from 7.0-11.0% to 7.5-10.5% based on feasibility data"
  ],
  "recruitment_metrics": {
    "estimated_screen_success_rate": 0.35,
    "estimated_enrollment_rate": 0.65,
    "key_barriers": ["HbA1c upper limit", "concomitant medication restrictions"]
  }
}

Criteria Categories

Category	Description	Examples
demographics	Age, sex, race, ethnicity	Age 18-75, women of childbearing potential
disease_severity	Disease stage, severity markers	HbA1c range, tumor stage, NYHA class
medical_history	Prior conditions, comorbidities	No cardiovascular events within 6 months
concomitant_meds	Allowed/prohibited medications	Stable metformin dose allowed
laboratory	Lab value requirements	eGFR > 30 mL/min, normal liver function
lifestyle	Diet, exercise, habits	Non-smoker, willing to maintain diet
compliance	Ability to participate	Able to provide informed consent
safety	Risk minimization criteria	No history of severe hypoglycemia

Optimization Strategies

Common Modifications

Issue	Strategy	Example
Narrow age range	Widen limits	18-70 → 18-75 years
Restrictive lab values	Adjust thresholds	eGFR > 60 → eGFR > 30 mL/min
Comorbidity exclusions	Add time limits	Exclude "current" vs "history of"
Medication washouts	Shorten periods	4 weeks → 2 weeks
Geographic barriers	Add telemedicine	Include remote visits option

Retention Considerations

• Minimize visit frequency when possible
• Allow window periods for visit timing
• Provide transportation assistance language
• Consider patient-reported outcome burden

Technical Details

• Difficulty: Medium
• Standards: ICH E6(R2) GCP, CDISC Protocol Representation Model
• Data Sources: ClinicalTrials.gov eligibility patterns, literature feasibility data
• Dependencies: None (pure Python)

References

• references/criteria_templates.json - Templates by therapeutic area
• references/optimization_guidelines.md - Best practices for criteria optimization
• references/common_pitfalls.md - Frequent eligibility design mistakes
• references/regulatory_guidance.md - FDA/EMA guidance on eligibility criteria
• references/feasibility_data.json - Screen failure rates by criterion type

Security Checklist

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• API requests use HTTPS only
• Input validated against allowed patterns
• API timeout and retry mechanisms implemented
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no internal paths exposed)
• Dependencies audited
• No exposure of internal service architecture

Prerequisites

# Python dependencies
pip install -r requirements.txt

Parameters

Parameter	Type	Default	Description
--indication	str	Required	Therapeutic indication
--phase	str	Required
--population	str	"adults"	Target population
--duration	str	""	Study duration
--output	str	Required	Output file path
--age-min	int	18	Minimum age
--age-max	int	75	Maximum age
--input	str	Required	Input criteria JSON file
--enrollment-target	int	Required	Target enrollment
--current-enrollment	int	Required	Current enrollment
--output	str	Required	Output file path
--input	str	Required	Input criteria JSON file
--output	str	Required	Output file path
--input	str	Required	Input criteria JSON file
--condition	str	Required	Medical condition
--output	str	Required	Output file path

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of inclusion-criteria-gen and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

inclusion-criteria-gen only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

Response Template

Use the following fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.

When Not to Use

• Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
• Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
• Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.

Required Inputs

Field	Required	Format/Source	Example	If Missing
User task description	Yes	Text	Research question, writing goal, analysis objective	Stop and ask user to provide
Primary input material	Depends on task	Text, file path, ID, table, or literature	PMID, PDF, CSV, DOCX, keywords, etc.	Specify which material type is missing
Output preference	No	Text	Language, format, target journal, template	Use skill default format

Output Contract

• Primary output: Structured result or target file aligned with this skill's objective.
• Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths.
• Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format.
• If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain.

Failure Handling

• Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause.
• Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade.
• Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps.

User Checkpoints

• Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user.
• Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user.

Quick Validation

• Check that key scripts, templates, or reference file paths this skill depends on exist.
• Check that the final output contains the core fields, sections, or files specified for this task.
• Check that results clearly mark assumptions, limitations, and incomplete items.