DOEJGI/

GenomeOcean-4B-bgcFM

This is GenomeOcean-bgcFM, a model finetuned on biosynthetic gene clusters (BGC) sequences. It is built on GenomeOcean-4B. It is trained with Causal Language Modeling (CLM) and uses a BPE tokenizer with 4096 tokens. It supports a maximum sequence length of 10240 tokens (~50kbp).

Please see our official implementation on our Github.

Quick start.

import torch
from transformers import AutoModelForCausalLM, AutoTokenizer

tokenizer = AutoTokenizer.from_pretrained(
    "pGenomeOcean/GenomeOcean-4B-bgcFM",
    trust_remote_code=True,
    padding_side="left",
)
model = AutoModelForCausalLM.from_pretrained(
    "pGenomeOcean/GenomeOcean-4B-bgcFM",
    trust_remote_code=True,
    torch_dtype=torch.bfloat16, 
    attn_implementation="flash_attention_2",
).to("cuda") 

Copyright Notice

genomeocean: a pretrained microbial genome foundational model (genomeoceanLLM) ” Copyright (c) 2025, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and Northwestern University. All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at IPO@lbl.gov.

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.