molly-bioinformatics

Molly Specialist — Bioinformatics

Produces correct command-line invocations for bioinformatics tools (BWA, samtools, bcftools) and accurately interprets VCF, BAM, and FASTA file formats better than the base model.

Part of Molly, an orchestrator that keeps a library of small domain specialists over one quantized base and routes each request to the right one, so a single machine answers across many fields without loading a separate large model for each.

What this specialist handles well

• Generating correct BWA and samtools command lines with proper flags
• Interpreting VCF variant records and predicting functional protein effects
• Explaining FASTQ quality encoding and read-pair orientation conventions

Try it with

• "How do I filter a VCF for variants with quality above 30 and depth above 10?"
• "What does the MAPQ field in a BAM file represent and how is it calculated?"
• "Which BWA-MEM flags should I use for paired-end 150bp Illumina reads?"

Before you run: the base model is gated

This adapter needs the base weights, and the base is access-gated. Do this once:

1. Accept the base licence: https://huggingface.co/meta-llama/Llama-3.1-8B-Instruct
2. Create a read token: https://huggingface.co/settings/tokens
3. Make the token available:
   • Google Colab: Secrets panel (key icon) → Add new secret → name HF_TOKEN, enable Notebook access.
   • Kaggle: Add-ons → Secrets → add HF_TOKEN.
   • Local: huggingface-cli login or export HF_TOKEN=...

Skipping this gives GatedRepoError / 401 Unauthorized when the base loads. A stored Colab secret is not applied automatically — authenticate in code, as below.

Quickstart

# pip install -U transformers peft accelerate
import os, torch
from huggingface_hub import login
try:
    from google.colab import userdata
    login(userdata.get("HF_TOKEN"))
except Exception:
    tok = os.environ.get("HF_TOKEN")
    login(tok) if tok else login()

from transformers import AutoModelForCausalLM, AutoTokenizer
from peft import PeftModel

BASE = "meta-llama/Llama-3.1-8B-Instruct"
ADAPTER = "BoomJules/molly-bioinformatics"

tok = AutoTokenizer.from_pretrained(BASE)
base = AutoModelForCausalLM.from_pretrained(BASE, torch_dtype=torch.bfloat16, device_map="auto")
model = PeftModel.from_pretrained(base, ADAPTER).eval()

msgs = [{"role": "user", "content": "Your question here"}]
ids = tok.apply_chat_template(msgs, add_generation_prompt=True, return_tensors="pt").to(model.device)
out = model.generate(ids, max_new_tokens=300)
print(tok.decode(out[0][ids.shape[1]:], skip_special_tokens=True))

Low-VRAM (4-bit) — fits a free Colab/Kaggle GPU (~6–7 GB)

# pip install -U transformers peft accelerate bitsandbytes
import os, torch
from huggingface_hub import login
try:
    from google.colab import userdata
    login(userdata.get("HF_TOKEN"))
except Exception:
    login(os.environ.get("HF_TOKEN"))

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

bnb = BitsAndBytesConfig(load_in_4bit=True, bnb_4bit_quant_type="nf4",
                         bnb_4bit_compute_dtype=torch.bfloat16, bnb_4bit_use_double_quant=True)
tok = AutoTokenizer.from_pretrained("meta-llama/Llama-3.1-8B-Instruct")
base = AutoModelForCausalLM.from_pretrained("meta-llama/Llama-3.1-8B-Instruct", quantization_config=bnb, device_map="auto")
model = PeftModel.from_pretrained(base, "BoomJules/molly-bioinformatics").eval()

Adapter details

Troubleshooting

• GatedRepoError / 401 Unauthorized — base licence not accepted, or HF_TOKEN missing, or the Colab secret was stored but login(...) was never called.
• CUDA out of memory — use the 4-bit snippet on a GPU runtime.
• Adapter seems to have no effect — confirm the base id matches base_model above.

Other Molly specialists

• Quantum Software Architect
• Quantum Communication Systems Engineer
• Infectious Disease Physician Antimicrobial Stewardship
• Health Informatics Medical AI Specialist
• Clinical Trial Pharmacologist
• Immunopharmacologist
• Climate Analytics Manager
• Language Technology Consultant
• Polymer Chemist
• Composite Materials Engineer
• Computer Science AI
• Computer Science Algorithms

Running several of these at once, with the routing decided for you, is what Molly does.

Licence & intended use

Adapter: CC BY-NC 4.0 (attribution, non-commercial). Base model: its own licence. Intended for research and evaluation in Bioinformatics.

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