Icd10 Cpt Coding Assistant

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

ICD-10 & CPT Coding Assistant

A medical coding assistant that parses clinical notes and recommends appropriate ICD-10 diagnosis codes and CPT procedure codes with confidence scoring.

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 --input "Audit validation sample with explicit symptoms, history, assessment, and next-step plan." --format json

When to Use

• Recommending ICD-10 diagnosis codes from clinical documentation
• Suggesting CPT procedure codes for billing and documentation
• Cross-referencing diagnoses with procedure codes
• Quality-checking existing code assignments

Workflow

1. Parse clinical note — Input: clinical note text (free-text, SOAP, discharge summary, progress note) → extract diagnoses, procedures, symptoms → Output: structured clinical entities
2. Map to ICD-10-CM — Match diagnoses to ICD-10 codes → compute confidence scores (0.0-1.0) → generate alternatives for medium-confidence codes → Output: ICD-10 recommendation list with evidence
3. Map to CPT — Match procedures/services to CPT codes → determine E/M level if applicable → Output: CPT recommendation list with time/complexity
4. Filter by confidence — Apply --confidence-threshold (default 0.7) → separate high/medium/low confidence recommendations → ⛔ Checkpoint: Present low-confidence codes (<0.7) to user for manual review; confirm all codes before output → Output: filtered code set
5. Generate report — Format as JSON or text per --format flag → include evidence trail, alternatives, and human-review flags → Output: final coding report

Overview

This skill analyzes clinical documentation to extract relevant medical information and map it to standardized coding systems:

• ICD-10-CM: International Classification of Diseases, 10th Revision, Clinical Modification (diagnosis codes)
• CPT: Current Procedural Terminology (procedure/service codes)

Technical Difficulty: HIGH ⚠️

⚠️ HUMAN REVIEW REQUIRED: Medical coding directly impacts billing, reimbursement, and clinical documentation. All recommendations must be verified by a certified medical coder or healthcare provider.

Usage

python scripts/main.py --input "clinical_note.txt" [--format json|text]

Or use programmatically:

from scripts.main import CodingAssistant

assistant = CodingAssistant()
result = assistant.analyze("Patient presents with acute bronchitis...")
print(result.icd10_codes)
print(result.cpt_codes)

Parameters

Input Format

Accepts clinical notes in various formats:

• Free-text narrative
• SOAP notes (Subjective, Objective, Assessment, Plan)
• Discharge summaries
• Progress notes
• Procedure reports

Output Format

ICD-10 Recommendations

{
  "icd10_codes": [
    {
      "code": "J20.9",
      "description": "Acute bronchitis, unspecified",
      "confidence": 0.92,
      "evidence": ["cough for 5 days", "wheezing on exam"],
      "alternatives": ["J20.0", "J44.9"]
    }
  ]
}

CPT Recommendations

{
  "cpt_codes": [
    {
      "code": "99213",
      "description": "Office visit, established patient, moderate complexity",
      "confidence": 0.85,
      "evidence": ["detailed history", "low complexity decision making"],
      "time": "20 minutes"
    }
  ]
}

Confidence Scoring

• 0.90-1.00: High confidence - Clear documentation, unambiguous mapping
• 0.70-0.89: Medium confidence - Good documentation, some interpretation required
• 0.50-0.69: Low confidence - Incomplete documentation, multiple possibilities
• <0.50: Very low confidence - Insufficient information, manual review essential

Limitations

1. No Medical Advice: This tool does not provide clinical advice or diagnoses
2. Coding Complexity: Cannot handle all coding nuances (comorbidities, sequencing, modifiers)
3. Regional Variations: May not account for payer-specific coding requirements
4. Updates: Code sets may not reflect the latest annual updates

References

See references/ folder for:

• icd10_common_codes.json: Frequently used ICD-10 codes by specialty
• cpt_common_codes.json: Frequently used CPT codes by specialty
• coding_guidelines.md: General coding guidelines and conventions

Safety & Compliance

• HIPAA Awareness: Ensure de-identification of PHI before processing
• Audit Trail: Maintain records of automated recommendations for compliance
• Human Oversight: All codes must be reviewed and approved by qualified personnel

Dependencies

• Python 3.8+
• See requirements.txt for package dependencies

Risk Assessment