🧠 ClinicalBERT-MS-Autoimmune-Neuro

A fine-tuned version of emilyalsentzer/Bio_ClinicalBERT
for detecting autoimmune neurological disease signals from clinical text notes.

Maintainer: Vahid Mahmoudian
Repository: vhdm/clinicalbert-ms-autoimmune-neuro
Status: Research / Proof-of-Concept — not for standalone clinical use

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🔍 Model Summary

Property	Value
Base model	emilyalsentzer/Bio_ClinicalBERT
Task	Binary text classification (autoimmune-neurological vs non-autoimmune)
Language	English clinical notes
Domain	Neurology / Autoimmune disorders
Dataset	Internal “MS-autoimmune” corpus (split into train, valid, test)
Sequence length	512 tokens per chunk
Hardware	NVIDIA H100
Mixed precision	bf16
Trainer seed	42
Epochs	4
Learning rate	2 × 10⁻⁵
Optimizer	adamw_torch
Batch sizes	train = 24, eval = 48
Warmup ratio	0.1
Best metric	recall

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⚙️ Training Log (chunk-level)

Below metrics are auto-generated by Hugging Face Trainer
using the raw validation set (before note aggregation, calibration, or threshold tuning).

Step	Train Loss	Val Loss	Accuracy	Precision	Recall	F1	AUC
200	0.655	0.627	0.660	0.800	0.0377	0.0720	0.6259
800	0.331	0.373	0.840	0.882	0.628	0.733	0.8856
1600	0.275	0.360	0.851	0.854	0.691	0.764	0.9040
2400	0.291	0.333	0.858	0.878	0.689	0.772	0.9121
3400	0.220	0.358	0.861	0.851	0.731	0.786	0.9169
4600	0.169	0.432	0.856	0.828	0.744	0.784	0.9172

Final Trainer metrics (chunk-level):

These are raw chunk-level metrics for monitoring during training — not the final evaluation used for deployment.

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🧩 Note-Level Aggregated Evaluation (final tuned results)

After post-processing with:

• Aggregation: logit_topk (k = 3)
• Calibration: temperature scaling (T = 1.372)
• Threshold: tuned on validation (Fβ = 1.5 → thr ≈ 1.000)
• Inference logic: per-note probability = mean(logit(top-k chunks))

Validation (n = 493)

Metric	Value
Precision	0.9118
Recall	0.9394
F1	0.9254
Accuracy	0.9493
ROC-AUC	0.9688

Test (n = 493)

Metric	Value
Precision	0.9618
Recall	0.9207
F1	0.9408
Accuracy	0.9615
ROC-AUC	0.9786

✅ Final configuration:
Aggregation = logit_topk(k=3) Temperature = 1.372 Threshold ≈ 1.0

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🧠 Inference Example

from transformers import AutoTokenizer, AutoModelForSequenceClassification
import torch, numpy as np

repo = "vhdm/clinicalbert-ms-autoimmune-neuro"
tok = AutoTokenizer.from_pretrained(repo)
model = AutoModelForSequenceClassification.from_pretrained(repo)

texts = ["Patient reports numbness in lower limbs...", "MRI shows demyelination consistent with MS."]
inputs = tok(texts, padding=True, truncation=True, return_tensors="pt")

with torch.no_grad():
    logits = model(**inputs).logits
probs = torch.softmax(logits, dim=-1).numpy()[:, 1]

# logit_topk aggregation (k=3)
probs = np.clip(probs, 1e-6, 1-1e-6)
logits_ = np.log(probs) - np.log(1-probs)
k = 3
idx = np.argsort(logits_)[-min(k, len(logits_)):]
mean_logit = logits_[idx].mean()
note_score = 1.0 / (1.0 + np.exp(-mean_logit))

T = 1.372  # temperature
note_score_cal = 1.0 / (1.0 + np.exp(-mean_logit / T))
thr = 1.0  # tuned threshold

pred = int(note_score_cal >= thr)
print({"score": note_score_cal, "prediction": pred})

🧪 Reproducibility

TrainingArguments(
  output_dir="./runs/clinicalbert_ms",
  learning_rate=2e-5,
  per_device_train_batch_size=24,
  per_device_eval_batch_size=48,
  num_train_epochs=5,
  weight_decay=0.01,
  bf16=True,
  optim="adamw_torch",
  warmup_ratio=0.1,
  seed=42,
  evaluation_strategy="steps",
  save_strategy="steps",
  logging_steps=50,
  eval_steps=200,
  save_steps=200,
  save_total_limit=3,
  load_best_model_at_end=True,
  metric_for_best_model="recall",
  greater_is_better=True,
)