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aicliniq

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Open-source AI agent framework for healthcare and life sciences

agentsaiclinicaldrug-discoveryfhirhealthcarehipaallm
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README

Version 0.1.0a0 documentation

AICliniq

The open-source Python framework for building healthcare AI applications.
Like Django is to web apps, like HuggingFace is to ML models, AICliniq is to clinical AI.

Created and maintained by Satheesh Kola.

CI Python 3.11+ License: Apache 2.0

Install the framework. Use pre-built clinical agents. Build your healthcare AI product in days.


What is AICliniq?

AICliniq is a 5-layer framework for healthcare AI:

Layer 1: Core Framework      → pip install aicliniq
Layer 2: Domain Packs         → pip install aicliniq[clinical]
Layer 3: Server               → aicliniq serve
Layer 4: Dashboard            → aicliniq ui
Layer 5: CLI Scaffolding      → aicliniq new my-app

17 clinical domains · 39 model providers · LLM Council (multi-model consensus) · MCP Server · HIPAA audit trail · FHIR R4 · 4 memory types · 6 reasoning patterns · 7 safety layers

New to AICliniq? Read ARCHITECTURE.md to understand the 5-layer framework model.

Quick Start — 5 Levels

Level 1: Beginner (3 lines, 5 minutes)

pip install aicliniq[groq]
export GROQ_API_KEY=gsk_...
from aicliniq import quick
import asyncio

# Clinical scribe — transcript to SOAP note
note = asyncio.run(quick.scribe("Patient is a 45yo male with chest pain..."))
print(note.soap)

# Triage — symptoms to urgency classification
result = asyncio.run(quick.triage("chest pain, diaphoresis", age=62))
print(f"{result.urgency} ({result.score}/10)")

# Clinical Q&A — evidence-based answers
answer = asyncio.run(quick.ask("First-line treatment for HFrEF?"))
print(answer.answer)

Level 2: Builder (use pre-built domain agents)

pip install aicliniq[clinical-radiology]
from aicliniq.domains.clinical.radiology import RadiologyReportAgent
from aicliniq.providers.vlm.medgemma import MedGemmaProvider

agent = RadiologyReportAgent(vlm=MedGemmaProvider())
report = await agent.run(input=dicom_image)
print(report.findings)

Level 3: Customizer (extend for your hospital)

from aicliniq.domains.clinical.radiology import RadiologyReportAgent

class CityGeneralRadiologyAgent(RadiologyReportAgent):
    """Customized for City General Hospital"""
    REPORT_TEMPLATE = CITY_GENERAL_TEMPLATE
    
    async def on_critical_finding(self, finding):
        await notify_slack(finding)

Level 4: Product Builder (scaffold full app)

aicliniq new my-radiology-saas --template radiology
cd my-radiology-saas
docker compose up -d
# Full FastAPI + React + Postgres app running

Level 5: Enterprise (self-hosted platform)

git clone https://github.com/kolasatheesh/aicliniq
cd aicliniq
docker compose up -d
# Postgres (pgvector) + FastAPI server + React console, all on your own infrastructure

I Want To...

GoalStart HereTime
Try it in 3 linesquick.py5 min
Build a radiology toolRadiologyReportAgent1 hour
Build a pharma trainerMedRepTrainingAgent2 hours
Build a patient portalPatientJourneyOrchestrator1 day
Build something customBaseAgent + AgentGraph2 days
Deploy for a hospitalDocker + Server Layer1 week

What's Inside

17 Clinical Domains (34+ Agents)

DomainAgents
CardiologyECG Interpreter, Cardiac Risk, Zodiac Pipeline
Emergency/ICUED Triage, ICU Supervisor, Sepsis Management Graph
SurgerySurgical Scribe, Pre-Op Assessment
OncologyTumor Board, Trial Matching
RadiologyRadiology Scribe, Imaging Triage
Primary CareIntake, Follow-Up, Screening
Drug DiscoveryTarget ID, Molecule Design, ADMET, Repurposing
PathologyPathology Scribe, Biopsy Triage
GenomicsVariant Interpretation, Pharmacogenomics
+ 8 morePharmacovigilance, Digital Health, Clinical Trials, Operations, Population Health, Med Education, Compliance, Pharma Ops

39 Model Providers

LLM (24): Groq, OpenAI, Anthropic, Gemini, DeepSeek, xAI/Grok, Cohere, Mistral, Fireworks, Together, HuggingFace, LiteLLM, Ollama, + 11 more VLM (3): MedGemma 1.5, PathChat+, BiomedCLIP Genomics (2): ESM-2 (proteins), Enformer (gene expression) Chemistry (2): ChemBERTa, RDKit Speech (6): Whisper, AssemblyAI, ElevenLabs, Google STT, Azure Speech, Kokoro

Production Platform

LayerWhat it does
LLM CouncilMulti-model consensus with 4 modes, PHI-aware routing, confidence scoring
ObservabilityLangfuse + OpenTelemetry tracing, cost tracking, drift detection
Safety (7 layers)PHI masking, AES-256 encryption, sandboxed execution, HITL, scope constraints, hallucination guard, audit trail
ExplainabilitySHAP, narrative explanations, attention visualization
Memory (4 types)Working, episodic (learns from feedback), semantic (pgvector), procedural (clinical playbooks)
Reasoning (6 patterns)ReAct, CoT, Plan-and-Execute, ReWOO, Swarm, Council
ProtocolsMCP Server (plug into Claude/Cursor), A2A (cross-framework agents)
Federated LearningTrain across hospitals without sharing data (Flower + Opacus)
Voice AIAmbient scribe, conversational voice agent
Fine-TuningLoRA/QLoRA trainer, data curator, model registry
InteroperabilitySMART on FHIR, HL7 v2, CDA, SNOMED/LOINC/ICD-10 terminology
BenchmarksMedAgentBench (Stanford), AgentDS Healthcare

Full-Stack Application

  • FastAPI server — 11 API routers (50+ endpoints), JWT auth, multi-tenant, SSE streaming
  • React console — 28 pages covering every clinical domain + LLM Council
  • PostgreSQL + pgvector — semantic search and long-term memory
  • Docker Compose — one-command deployment

CLI

aicliniq serve          # Start API server
aicliniq ui             # Start React console
aicliniq agents         # List all 34+ agents
aicliniq domains        # List all 17 domains
aicliniq init           # Generate starter project
aicliniq sandbox        # Explore synthetic clinical data
aicliniq learn          # Interactive tutorials
aicliniq run scribe -i '{"transcript": "..."}'  # Run agent from CLI
aicliniq validate       # Check configuration

v0.1.0-alpha Status

Covered by Tests (1,800+ automated tests, LLM calls mocked)

  • All template agents (Scribe, Triage, RAG-QA, Diagnostic Dialogue)
  • LLM Council (25 tests: consensus, PHI routing, agreement scoring)
  • Groq and OpenAI LLM providers
  • PHI Masker, AES-256 encryption, sandbox, hallucination guard
  • FHIR R4 resources (all 11 types), HL7 v2 parser, terminology service
  • Observability (tracing, cost tracking, drift detection)
  • Full server test suite (auth, agents, audit, compliance, multitenancy, FHIR)

Scaffolded (Contributions Welcome)

  • 22 of 39 providers (stubs with clear error messages — see PROVIDERS.md)
  • Federated learning, voice AI, fine-tuning (architecture ready)

Documentation

Full documentation at docs.aicliniq.org: concepts, platform layers, guides, deployment, and persona-specific onboarding.

For the complete usage guide including how to run, build, package, and deploy: HOW_TO_USE.md

Contributing

See CONTRIBUTING.md. We especially welcome:

  • New clinical domain packs
  • Provider implementations
  • Evaluation benchmarks
  • Translations (10 languages supported)

License

Copyright 2026 Satheesh Kola. Licensed under the Apache License 2.0; see NOTICE.

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