Instructions to use Babajaan/KAU-BioMedLLM with libraries, inference providers, notebooks, and local apps. Follow these links to get started.

Libraries

How to use Babajaan/KAU-BioMedLLM with Transformers:

# Use a pipeline as a high-level helper
from transformers import pipeline

pipe = pipeline("text-generation", model="Babajaan/KAU-BioMedLLM")
messages = [
    {"role": "user", "content": "Who are you?"},
]
pipe(messages)

# Load model directly
from transformers import AutoModel
model = AutoModel.from_pretrained("Babajaan/KAU-BioMedLLM", device_map="auto")

Notebooks
Google Colab
Kaggle
Local Apps Settings

vLLM

How to use Babajaan/KAU-BioMedLLM with vLLM:

Install from pip and serve model

# Install vLLM from pip:
pip install vllm
# Start the vLLM server:
vllm serve "Babajaan/KAU-BioMedLLM"
# Call the server using curl (OpenAI-compatible API):
curl -X POST "http://localhost:8000/v1/chat/completions" \
	-H "Content-Type: application/json" \
	--data '{
		"model": "Babajaan/KAU-BioMedLLM",
		"messages": [
			{
				"role": "user",
				"content": "What is the capital of France?"
			}
		]
	}'

Use Docker

docker model run hf.co/Babajaan/KAU-BioMedLLM

SGLang

How to use Babajaan/KAU-BioMedLLM with SGLang:

Install from pip and serve model

# Install SGLang from pip:
pip install sglang
# Start the SGLang server:
python3 -m sglang.launch_server \
    --model-path "Babajaan/KAU-BioMedLLM" \
    --host 0.0.0.0 \
    --port 30000
# Call the server using curl (OpenAI-compatible API):
curl -X POST "http://localhost:30000/v1/chat/completions" \
	-H "Content-Type: application/json" \
	--data '{
		"model": "Babajaan/KAU-BioMedLLM",
		"messages": [
			{
				"role": "user",
				"content": "What is the capital of France?"
			}
		]
	}'

Use Docker images

docker run --gpus all \
    --shm-size 32g \
    -p 30000:30000 \
    -v ~/.cache/huggingface:/root/.cache/huggingface \
    --env "HF_TOKEN=<secret>" \
    --ipc=host \
    lmsysorg/sglang:latest \
    python3 -m sglang.launch_server \
        --model-path "Babajaan/KAU-BioMedLLM" \
        --host 0.0.0.0 \
        --port 30000
# Call the server using curl (OpenAI-compatible API):
curl -X POST "http://localhost:30000/v1/chat/completions" \
	-H "Content-Type: application/json" \
	--data '{
		"model": "Babajaan/KAU-BioMedLLM",
		"messages": [
			{
				"role": "user",
				"content": "What is the capital of France?"
			}
		]
	}'

Docker Model Runner
How to use Babajaan/KAU-BioMedLLM with Docker Model Runner:
```
docker model run hf.co/Babajaan/KAU-BioMedLLM
```

KAU-BioMedLLM / reports /DATA_PROVENANCE.md

Babajaan

Resolve resource versions (UniProt 2026_02, AlphaFold v6, Ensembl 116) + Llama-3.1 license compliance ('Built with Llama')

8a58482 verified 3 months ago

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KAUBioMED-LLM Data Provenance

Date prepared: 2026-06-15

This file records sources actually present or used in the HPC project. Unknown versions are explicitly marked as not recorded rather than guessed.

ClinVar Snapshots

ClinVar train snapshot

Path: /ddn/data/generic/bbabajan/KAUBioMED_LLM/data/raw/clinvar/archive_2.0/2023/clinvar_20231226.vcf.gz
Exists: True
Size bytes: 90917025
MD5: c1c17cb968c413c1809cb445347f051f
URL: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2023/clinvar_20231226.vcf.gz

ClinVar future/test snapshot

Path: /ddn/data/generic/bbabajan/KAUBioMED_LLM/data/raw/clinvar/archive_2.0/2025/clinvar_20251221.vcf.gz
Exists: True
Size bytes: 181881189
MD5: 0e9b0df5bc2f82334df20a3c61dd2494
URL: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2025/clinvar_20251221.vcf.gz

ClinVar Tab-Delimited Metadata

variant_summary.txt.gz

Path: /ddn/data/generic/bbabajan/KAUBioMED_LLM/data/raw/clinvar/variant_summary.txt.gz
Exists: True
Size bytes: 439336125
MD5: 0b1abcb00498745b05236fa7f7612b8c
URL: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz

submission_summary.txt.gz

Path: /ddn/data/generic/bbabajan/KAUBioMED_LLM/data/raw/clinvar/submission_summary.txt.gz
Exists: True
Size bytes: 381965640
MD5: 8926e17b9911c6388b2363c268d8de8e
URL: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/submission_summary.txt.gz

Allele Frequency Sources

gnomAD: not used in the current score_model feature table.
Current model uses ClinVar VCF INFO fields AF_ESP, AF_EXAC, and AF_TGP when present.
gnomAD version: not applicable for current results.

UniProt / PubMed Evidence

Evidence file: /ddn/data/generic/bbabajan/KAUBioMED_LLM/knowledge/kaubiomed_gene_evidence.jsonl
Exists: True
Size bytes: 253848
Access date: 2026-06-15 (HPC file mtime; queried via rest.uniprot.org/uniprotkb).
UniProt release: 2026_02 (released 10-Jun-2026), the release live on the access date. Resolved 2026-06-19 from UniProt relnotes; release was not captured at runtime.
Scope: 20-gene evidence panel, not genome-wide.

AlphaFold DB

Manifest: /ddn/data/generic/bbabajan/KAUBioMED_LLM/knowledge/alphafold/alphafold_manifest.jsonl
Exists: True
Size bytes: 12754
Access date: 2026-06-15 (HPC file mtime).
AlphaFold DB model version: v6 (from structure URLs, e.g. AF-P32245-F1-model_v6.cif). Note: an earlier evidence-builder pass fetched model_v4; final structures were refreshed to v6, which the manifest reflects.

Ensembl VEP REST

Mapper script: /ddn/data/generic/bbabajan/KAUBioMED_LLM/pipeline/vep_residue_mapper.py
Exists: True
Access date: 2026-06-15 (residue-mapping output mtime; rest.ensembl.org/vep/human/region, assembly GRCh38).
Ensembl release: 116 (REST API 15.12), the current live release. Resolved 2026-06-19 from rest.ensembl.org/info; release was not captured at runtime.
Mapping policy: MANE-preferred, HGVS protein required, UniProt reconciliation required, abstain on mismatch.

Base LLM Snapshots

Qwen2.5-1.5B-Instruct

Snapshot path: /ddn/data/generic/bbabajan/KAUBioMED_LLM/models/hf_snapshots/Qwen__Qwen2.5-1.5B-Instruct
Exists: True
Recorded revision: revision not recorded
Base model ID: Qwen/Qwen2.5-1.5B-Instruct
License: verify before public release.

Llama-3.1-8B-Instruct

Snapshot path: /ddn/data/generic/bbabajan/KAUBioMED_LLM/models/hf_snapshots/meta-llama__Llama-3.1-8B-Instruct
Exists: True
Recorded revision: revision not recorded
Base model ID: meta-llama/Llama-3.1-8B-Instruct
License: Meta Llama 3.1 Community License applies to Llama-derived adapter/merged artifacts; verify current license text before public release.

Score Model Feature Boundaries

Manuscript-facing score_model features exclude AlphaMissense, REVEL, CADD, UVPS, KAUBioMED LLM scores, ClinVar clinical-significance text, and ClinVar review-status/review_stars.