shabawak/ClinicalBERT-ColBERT

Medical Dense Retriever (Fine-tuned on Triplets)

This is a fine-tuned medicalai/ClinicalBERT model trained on medical question-answer triplets using the abhinand/MedEmbed-training-triplets-v1 dataset.

Dataset

• Source: abhinand/MedEmbed-training-triplets-v1
• Format: (query, positive passage, negative passage)
• Size: Subsampled to 1000 triplets for demonstration

Model Architecture

• Based on: ClinicalBERT (or similar encoder)
• Uses ColBERT's late interaction (MaxSim)
• Trained with triplet loss

Training Configuration

Parameter	Value	Description
base_model	medicalai/ClinicalBERT	Pretrained model used
interaction	colbert	Late interaction for dense retrieval
embedding_dim	128	Vector dimension per token
similarity	cosine	Scoring method
doc_maxlen	256	Max length of document input
query_maxlen	32	(From config or defaults)
batch_size	32 (global)	Effective total batch size
per_gpu_batch_size	16	Because nranks = 2
accum_steps	1	Gradient accumulation
learning_rate	5e-6	Optimizer learning rate
max_steps	500000	Training cutoff
warmup_steps	auto	Defaults to 10% of total steps
use_ib_negatives	True	In-batch negatives for training
use_relu	False	Disabled (default for ColBERT)
nbits	4	Index compression (Product Quantization)
AMP	True	Mixed precision training
gpus	2	Multi-GPU training
nranks	2	Distributed ranks (1 per GPU)

Intended Use

Dense retrieval for:

• Medical Q&A
• Biomedical semantic search
• Clinical decision support

🧪 How to Use

shabawak/ClinicalBERT-colbert-finetuned-ragatouille using RAGatouille

ClinicalBERT-colbert-finetuned-ragatouille operates using ColBERT + RAGatouille. To install it along with its dependencies, run:

pip install -U ragatouille

Using Bio_Clinical_ColBERT-finetuned Without an Index

For in-memory searching, simply:

1. Load the model
2. Encode documents
3. Search using search_encoded_documents()

from ragatouille import RAGPretrainedModel
RAG = RAGPretrainedModel.from_pretrained("shabawak/ClinicalBERT-colbert-finetuned-ragatouille")

RAG.encode(['document_1', 'document_2', ...])
RAG.search_encoded_documents(query="your search query")

• New encode() calls append to the existing collection.
• Clear stored docs with RAG.clear_encoded_docs().

Indexing Documents

ColBERT's late-interaction retrieval requires indexing first. This step is slow, but retrieval is fast.

from ragatouille import RAGPretrainedModel  

RAG = RAGPretrainedModel.from_pretrained("shabawak/ClinicalBERT-colbert-finetuned-ragatouille")  
documents = ['document_1', 'document_2', ...]  # Your documents  
RAG.index(name="My_first_index", collection=documents)  

• Index files are saved in .ragatouille/colbert/indexes/{index_name} by default.

Searching an Index

After indexing, querying is straightforward. If reopening a session, load the index first:

RAG = RAGPretrainedModel.from_index(".ragatouille/colbert/indexes/My_first_index")  
results = RAG.search(query="What is the expected outcome for a patient diagnosed with D-2-hydroxyglutaric aciduria type I?",k=5)

• The results include content, relevance scores, rankings, and metadata (if provided).

[[{'content': 'In April 1984, Miyazaki opened his own office in Suginami Ward, naming it Nibariki.\n\n\n=== Studio Ghibli ===\n\n\n==== Early films (1985–1996) ====\nIn June 1985, Miyazaki, Takahata, Tokuma and Suzuki founded the animation production company Studio Ghibli, with funding from Tokuma Shoten. Studio Ghibli\'s first film, Laputa: Castle in the Sky (1986), employed the same production crew of Nausicaä. Miyazaki\'s designs for the film\'s setting were inspired by Greek architecture and "European urbanistic templates".',
   'score': 25.90448570251465,
   'rank': 1,
   'document_id': 'miyazaki',
   'document_metadata': {'entity': 'person', 'source': 'wikipedia'}},
  {'content': 'Hayao Miyazaki (宮崎 駿 or 宮﨑 駿, Miyazaki Hayao, Japanese: [mijaꜜzaki hajao]; born January 5, 1941) is a Japanese animator, filmmaker, and manga artist. A co-founder of Studio Ghibli, he has attained international acclaim as a masterful storyteller and creator of Japanese animated feature films, and is widely regarded as one of the most accomplished filmmakers in the history of animation.\nBorn in Tokyo City in the Empire of Japan, Miyazaki expressed interest in manga and animation from an early age, and he joined Toei Animation in 1963. During his early years at Toei Animation he worked as an in-between artist and later collaborated with director Isao Takahata.',
   'score': 25.572620391845703,
   'rank': 2,
   'document_id': 'miyazaki',
   'document_metadata': {'entity': 'person', 'source': 'wikipedia'}},
  {'content': 'Glen Keane said Miyazaki is a "huge influence" on Walt Disney Animation Studios and has been "part of our heritage" ever since The Rescuers Down Under (1990). The Disney Renaissance era was also prompted by competition with the development of Miyazaki\'s films. Artists from Pixar and Aardman Studios signed a tribute stating, "You\'re our inspiration, Miyazaki-san!"',
   'score': 24.84041976928711,
   'rank': 3,
   'document_id': 'miyazaki',
   'document_metadata': {'entity': 'person', 'source': 'wikipedia'}}]]