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batch_rgb_benchmark.py
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batch_rgb_benchmark.py
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# -*- coding: utf-8 -*-
# file: batch_rgb_benchmark.py
# time: 13:26 04/06/2024
# author: YANG, HENG <[email protected]> (杨恒)
# github: https://github.com/yangheng95
# huggingface: https://huggingface.co/yangheng
# google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
# Copyright (C) 2019-2024. All Rights Reserved.
import argparse
import random
from omnigenome import AutoBench
if __name__ == "__main__":
gfms = [
"genomic_foundation_models/OmniGenomeV3-186M",
# "genomic_foundation_models/OmniGenomeV2-186M",
# "anonymous8/OmniGenome-186M",
# "genomic_foundation_models/SpliceBERT-510nt",
# "genomic_foundation_models/DNABERT-2-117M",
# "genomic_foundation_models/3utrbert",
# "genomic_foundation_models/hyenadna-large-1m-seqlen-hf",
# "genomic_foundation_models/nucleotide-transformer-v2-100m-multi-species",
]
bench_root = "RGB"
bench_size = 4
seeds = [3407, 3408, 3409]
for gfm in gfms:
bench = AutoBench(bench_root=bench_root, model_name_or_path=gfm, overwrite=True)
bench.run(autocast=False, batch_size=bench_size, seeds=seeds)