RitanshuPatel/triageai-mistral

LoRA fine-tuned Mistral-7B for clinical notes extraction — converts messy doctor notes into structured JSON with consistent accuracy.

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The Problem We Are Solving

Every day, doctors and clinicians write hundreds of clinical notes that look like this:

pt 67M c/o CP x2hr rad to L arm, diaphoretic, SOB+, PMH DM2 HTN, 
smoker 20pk/yr, meds metformin 500 BID lisinopril 10 QD atorvastatin 
40 QHS, EKG ST elev V2-V4, trop pnd, A: r/o STEMI, allerg PCN hives

This is the reality of clinical documentation — abbreviated, unstructured, and nearly unreadable to anyone outside the medical field.

The core problems this creates:

• Abbreviations are ambiguous — CP can mean chest pain, cerebral palsy, or care plan depending on context. Base LLMs frequently get these wrong.

• Inconsistent JSON output — When you ask a base LLM to extract structured data from clinical notes, it returns different JSON structures every time. Sometimes conditions is a list of strings, sometimes a list of objects, sometimes nested. This breaks downstream applications.

• Missing critical fields — Base models skip medications, miss vitals, or hallucinate dosages that were never in the original note.

• Medical abbreviation blindness — Standard LLMs are not trained heavily on clinical shorthand. BID, QD, TID, PRN, c/o, PMH, r/o — these require specialized understanding.

• Time cost — A clinician manually transcribing and structuring one note takes 5-10 minutes. Multiply that by 50 patients a day and you have a significant administrative burden that takes time away from patient care.

The goal of this model is simple: paste any messy clinical note, get back perfectly structured JSON every single time.

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Why This Model is Outstanding

1. Trained on Real De-identified Clinical Notes

This model was fine-tuned on MTSamples — one of the most widely used datasets of real de-identified medical transcriptions covering 40+ medical specialties including cardiology, orthopedics, neurology, psychiatry, and general surgery. The training data reflects real-world clinical language, not synthetic examples.

2. Consistent JSON Structure Every Time

The biggest failure mode of base LLMs for clinical extraction is inconsistent output structure. After fine-tuning, this model returns the exact same JSON schema on every call:

{
  "patient": {"age": 67, "gender": "male"},
  "chief_complaint": "chest pain",
  "conditions": ["Hypertension", "Type 2 Diabetes"],
  "medications": [{"name": "metformin", "dose": "500mg", "frequency": "twice daily"}],
  "vitals": {"bp": "158/94", "hr": "102", "rr": null, "o2_sat": "94%"},
  "allergies": ["PCN"],
  "plan": []
}

No objects where strings are expected. No nested arrays. No missing fields. This consistency is what makes it production-ready for downstream applications.

3. Medical Abbreviation Mastery

Fine-tuning on clinical notes taught the model to correctly expand and interpret abbreviations that trip up base models:

Abbreviation	Correct Expansion
BID	twice daily
c/o	complains of
PMH	past medical history
r/o	rule out
HTN	Hypertension
DM2	Type 2 Diabetes
SOB	shortness of breath
STAT	immediately

4. Multi-Specialty Coverage

Training examples were carefully selected across 10 medical specialties to ensure the model generalizes well beyond a single domain:

• Cardiovascular / Cardiology
• Orthopedics / Surgery
• Neurology
• Endocrinology
• Pulmonology
• Psychiatry
• Gastroenterology
• Urology
• General Medicine
• Emergency Medicine

5. Efficient 4-bit Quantization

Trained using QLoRA (4-bit quantization) via BitsAndBytes — the model runs efficiently without requiring expensive GPU hardware. The LoRA adapter is only 13.6MB while the base model remains unchanged, making it easy to deploy anywhere Mistral-7B runs.

6. Genuine Learning — Not Just Memorization

Training loss dropped from 1.74 → 1.26 over 3 epochs, demonstrating genuine generalization to unseen clinical notes rather than memorizing training examples.

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Model Details

Property	Value
Base Model	mistralai/Mistral-7B-Instruct-v0.3
Fine-tuning Method	LoRA (Low-Rank Adaptation)
Quantization	QLoRA 4-bit (BitsAndBytes)
Adapter Size	13.6 MB
Training Platform	Google Colab T4 GPU (free tier)
Trainable Parameters	~0.5% of total parameters
Task	Clinical notes → Structured JSON
Language	English
License	MIT

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Training Data

Property	Value
Source	MTSamples (real de-identified clinical transcriptions)
Training Examples	49 carefully curated examples
Specialties	10 medical specialties
Format	JSONL instruction format (system / user / assistant)
Label Generation	llama-3.3-70b-versatile for high quality labels
Max Sequence Length	1024 tokens

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Training Configuration

LoraConfig(
    r=16,                          # LoRA rank
    lora_alpha=32,                 # LoRA alpha
    target_modules=["q_proj", "v_proj"],
    lora_dropout=0.1,
    bias="none",
    task_type="CAUSAL_LM"
)

TrainingArguments(
    num_train_epochs=3,
    per_device_train_batch_size=1,
    gradient_accumulation_steps=8,
    optim="paged_adamw_8bit",
    learning_rate=2e-4,
    fp16=False,
    bf16=False,
)

Training Loss Curve:

• Epoch 1: ~1.74
• Epoch 2: ~1.45
• Epoch 3: ~1.26

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How to Use

Load the adapter

from transformers import AutoModelForCausalLM, AutoTokenizer, BitsAndBytesConfig
from peft import PeftModel
import torch

# Load base model with 4-bit quantization
bnb_config = BitsAndBytesConfig(
    load_in_4bit=True,
    bnb_4bit_compute_dtype=torch.float16
)

base_model = AutoModelForCausalLM.from_pretrained(
    "mistralai/Mistral-7B-Instruct-v0.3",
    quantization_config=bnb_config,
    device_map="auto"
)

tokenizer = AutoTokenizer.from_pretrained(
    "mistralai/Mistral-7B-Instruct-v0.3"
)

# Load LoRA adapter
model = PeftModel.from_pretrained(
    base_model,
    "RitanshuPatel/triageai-mistral"
)

Run inference

SYSTEM_PROMPT = """You are a clinical notes parser.
Extract structured JSON from medical notes.
Return ONLY valid JSON with these fields:
{
  "patient": {"age": null, "gender": null},
  "chief_complaint": "",
  "conditions": [],
  "medications": [{"name": "", "dose": "", "frequency": ""}],
  "vitals": {"bp": null, "hr": null, "rr": null, "o2_sat": null},
  "allergies": [],
  "plan": []
}
Conditions and allergies must be plain strings. Never hallucinate."""

note = "pt 67M c/o CP x2hr, PMH DM2 HTN, metformin 500 BID lisinopril 10 QD, allerg PCN"

messages = [
    {"role": "system", "content": SYSTEM_PROMPT},
    {"role": "user", "content": note}
]

inputs = tokenizer.apply_chat_template(
    messages,
    return_tensors="pt"
).to(model.device)

outputs = model.generate(
    inputs,
    max_new_tokens=500,
    temperature=0.1,
    do_sample=True
)

result = tokenizer.decode(outputs[0], skip_special_tokens=True)
print(result)

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Performance Comparison

Base Mistral-7B output (inconsistent)

{
  "patient_info": {"age": "67 years old", "sex": "male"},
  "presenting_complaint": "chest pain for 2 hours",
  "past_history": [{"condition": "DM2"}, {"condition": "HTN"}],
  "current_medications": "metformin 500mg BID, lisinopril 10mg QD",
  "drug_allergies": [{"allergy": "PCN", "reaction": "unknown"}]
}

❌ Wrong field names, nested objects instead of strings, age as string not number

Fine-tuned output (consistent)

{
  "patient": {"age": 67, "gender": "male"},
  "chief_complaint": "chest pain",
  "conditions": ["Hypertension", "Type 2 Diabetes"],
  "medications": [
    {"name": "metformin", "dose": "500mg", "frequency": "twice daily"},
    {"name": "lisinopril", "dose": "10mg", "frequency": "once daily"}
  ],
  "vitals": {"bp": null, "hr": null, "rr": null, "o2_sat": null},
  "allergies": ["PCN"],
  "plan": []
}

✅ Correct schema, strings where expected, age as number, abbreviations expanded

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Intended Use & Medical Disclaimer

Intended for:

• Clinical NLP research and experimentation
• Building medical documentation tools
• Educational purposes
• Portfolio and demonstration projects

Not intended for:

• Direct clinical decision making
• Replacing qualified medical professionals
• Real patient care without human review

⚠️ Medical Disclaimer: This model is for informational and research purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment. All model outputs must be reviewed by qualified healthcare professionals before any clinical use.

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Part of the TriageAI Project

This model is the fine-tuned component of TriageAI — a full-stack clinical notes summarization agent.

Resource	Link
🌐 Live Demo	triageai-ritanshupatel.vercel.app
💻 GitHub	github.com/RitanshuPatelMMR/Triage-ai
🤗 HuggingFace Space	RitanshuPatel/triageai-backend

Full TriageAI Stack:

• LangGraph 5-node autonomous agent
• RAG with FAISS over 82,000+ medical knowledge vectors
• Real-time SSE streaming
• Groq Vision for handwritten note OCR
• OpenFDA drug interaction checking
• React + FastAPI frontend

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Built with ❤️ using Google Colab free T4 GPU, HuggingFace PEFT, and MTSamples dataset.