medgemma-competition/! at main · terraphim/medgemma-competition · GitHub

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╔══════════════════════════════════════════════════════════════╗
║                                                              ║
║   Terraphim Personalized Medicine System - Clinical Demo     ║
║   Full Patient Consultation Workflow                         ║
║                                                              ║
╚══════════════════════════════════════════════════════════════╝

[INITIALIZATION PHASE]
────────────────────────────────────────────────────────────
[OK] Entity extractor initialized
[OK] Knowledge Graph loaded (9 nodes, 7 edges)
[OK] PGx validator initialized (CPIC guidelines loaded)
[WARN] terraphim-llm-proxy not available, falling back to mock client
       (Proxy should be running at Proxy Client (http://127.0.0.1:3456))
[OK] MedGemma client initialized: Mock Client (healthy)


╔══════════════════════════════════════════════════════════════╗
║  CASE PRESENTATION: EGFR L858R Positive NSCLC               ║
╚══════════════════════════════════════════════════════════════╝

[STEP 1] PATIENT PRESENTATION
────────────────────────────────────────────────────────────
  Patient ID: DEMO-NSCLC-001
  Demographics: 58-year-old Male
  ECOG PS: 1
  Weight: 72.5 kg, Height: 175 cm

  Primary Diagnoses:
    - Stage IV adenocarcinoma of lung
    - EGFR L858R mutation positive
    - Brain metastases (new)

  Genomic Variants:
    - EGFR L858R: Activating mutation - sensitive to EGFR TKIs

  Current Medications:
    - Lisinopril 10mg Once daily
    - Gefitinib 250mg Once daily

  Clinical Note:
  "58-year-old male with EGFR L858R positive metastatic lung adenocarcinoma, progressed on first-line gefitinib therapy with new brain metastases, ECOG PS 1, no prior TKIs except gefitinib"

  [OK] Patient DEMO-NSCLC-001: 58-year-old Male, ECOG PS 1 (took 0.00ms)

[STEP 2] ENTITY EXTRACTION
────────────────────────────────────────────────────────────
Processing clinical note...
  Extracted 6 entities in 0.01ms:

  Genes/Variants (1):
    - EGFR (CUI: 363358001) - 100% confidence

  [OK] Extracted 6 entities: 0 diseases, 1 genes, 0 medications (took 0.01ms)

[STEP 3] KNOWLEDGE GRAPH QUERY
────────────────────────────────────────────────────────────
  No treatments found in Knowledge Graph

  [OK] Found 0 treatment options from Knowledge Graph (took 0.00ms)

[STEP 4] PHARMACOGENOMIC VALIDATION
────────────────────────────────────────────────────────────
  Pharmacogenomic Profile:
    - CYP3A4 (*1/*1): SAFE
    - CYP3A5 (*3/*3): SAFE
    - CYP2D6 (*1/*1): SAFE

  [OK] Completed 3 PGx validations (took 0.00ms)

[STEP 5] MEDGEMMA TREATMENT RECOMMENDATION
────────────────────────────────────────────────────────────
  PRIMARY RECOMMENDATION
  ────────────────────────
  Treatment: Osimertinib 80mg daily
  Confidence: 92%

  Clinical Reasoning:
  EGFR L858R mutation is sensitive to EGFR TKIs. Osimertinib is preferred first-line per FLAURA trial with demonstrated superior progression-free survival compared to first-generation EGFR TKIs.

  Alternative Options:
    - Erlotinib
    - Afatinib

  Supporting Evidence:
    - NCCN Guidelines NSCLC v4.2024
    - FLAURA Trial

  [OK] Recommended: Osimertinib 80mg daily (confidence: 92%) (took 101.46ms)

[STEP 6] SAFETY VALIDATION
────────────────────────────────────────────────────────────
  Safety Checks Performed:
    [PASS] Contraindications: No contraindications found
    [PASS] PGx Safety: All PGx validations passed
    [PASS] Confidence Threshold: Confidence: 92% (threshold: 80%)
    [PASS] Drug Allergies: No known allergy to recommended treatment

  [APPROVED] Safety validation PASSED - Ready for clinical review

  [OK] Safety validation PASSED - Ready for clinical review (took 0.01ms)


╔══════════════════════════════════════════════════════════════╗
║                    CONSULTATION SUMMARY                       ║
╚══════════════════════════════════════════════════════════════╝
  Patient: DEMO-NSCLC-001
  Total Processing Time: 101.59ms

  Workflow Steps:
    1. PatientPresented - 0.00ms
    2. EntitiesExtracted - 0.01ms
    3. KnowledgeGraphQueried - 0.00ms
    4. PGxValidated - 0.00ms
    5. TreatmentRecommended - 101.46ms
    6. SafetyValidated - 0.01ms

  Recommendation: Osimertinib 80mg daily
  Confidence: 92%

  [SUCCESS] Consultation complete - Treatment recommendation approved


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Demo complete. Press Enter to exit...