A comprehensive toolkit for DNA sequence Adversarial Attack and Defense Benchmark.
You can install GenoArmory using pip:
You can also install package from our source code:
git clone https://github.com/MAGICS-LAB/GenoArmory.gitconda create -n genoarmory pip=3.9pip install.
# Initialize modelfromGenoArmoryimportGenoArmoryimportjson# You need to initialize GenoArmory with a model and tokenizer.# For visualization, you don't need a real model/tokenizer, so you can use None if the method doesn't use them.gen=GenoArmory(model=None,tokenizer=None)params_file='/projects/p32013/DNABERT-meta/scripts/PGD/pgd_dnabert.json'# Visulizationgen.visualization(folder_path='/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test',output_pdf_path='/projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test')# Attackifparams_file:try:withopen(params_file,"r")asf:kwargs=json.load(f)exceptjson.JSONDecodeErrorase:raiseValueError(f"Invalid JSON in params file '{params_file}':{e}")exceptFileNotFoundError:raiseFileNotFoundError(f"Params file '{params_file}' not found.")gen.attack(attack_method='pgd',model_path='magicslabnu/GERM',**kwargs)GenoArmory can also be used from the command line:
# Attackpython GenoArmory.py --model_path magicslabnu/GERM attack --method pgd --params_file /projects/p32013/DNABERT-meta/scripts/PGD/pgd_dnabert.json# Defensepython GenoArmory.py --model_path magicslabnu/GERM defense --method at --params_file /projects/p32013/DNABERT-meta/scripts/AT/at_pgd_dnabert.json# Visualizationpython GenoArmory.py --model_path magicslabnu/GERM visualize --folder_path /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test --save_path /projects/p32013/DNABERT-meta/BERT-Attack/results/meta/test/frequency.pdf# Read MetaDatapython GenoArmory.py --model_path magicslabnu/GERMread --type attack --method TextFooler --model_name dnabert
Multiple attack methods:
- BERT-Attack
- TextFooler
- PGD
- FIMBA
Defense methods:
- ADFAR
- FreeLB
- Traditional Adversarial Training
Visualization tools
Artifact management
Batch processing
Command-line interface
For detailed documentation, visit [docs](We will release soon).
This project is licensed under the MIT License.
If you have any question regarding our paper or codes, please feel free to start an issue.
If you use GenoArmory in your work, please kindly cite our paper:
@misc{luo2025genoarmoryunifiedevaluationframework, title={GenoArmory: A Unified Evaluation Framework for Adversarial Attacks on Genomic Foundation Models}, author={Haozheng Luo and Chenghao Qiu and Yimin Wang and Shang Wu and Jiahao Yu and Han Liu and Binghui Wang and Yan Chen}, year={2025}, eprint={2505.10983}, archivePrefix={arXiv}, primaryClass={cs.LG}, url={https://arxiv.org/abs/2505.10983}, }
