GenBench: A Comprehensive Benchmark of genomic foundation models

Introduction

GenBench is a comprehensive benchmark for evaluating genomic foundation model, encompassing a broad spectrum of methods and diverse tasks, ranging from predicting gene location and function, identifying regulatory elements, and studying species evolution. GenBench offers a modular and extensible framework, excelling in user-friendliness, organization, and comprehensiveness. The codebase is organized into three abstracted layers, namely the core layer, algorithm layer, and user interface layer, arranged from the bottom to the top.

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Overview

Code Structures

• GenBench/configs contains configuration for benchmark evaluation.
• GenBench/data contains datasets.
• GenBench/notebook contains analysis and visualization notebooks.
• GenBench/src contains source code for evaluation piplines.
• GenBench/weight contains pretrained weights for benchmark evaluation.
• GenBench/experiment contains scripts for experiment management.

Installation

This project has provided an environment setting file of conda, users can easily reproduce the environment by the following commands:

cd GenBench
conda env create -f environment.yml
conda activate OpenGenome
python setup.py develop

Getting Started

Here is an example of single GPU non-distributed training HyenaDNA on demo_human_or_worm dataset.

bash tools/prepare_data/download_mmnist.sh
python train.py -m train experiment=hg38/genomic_benchmark_mamba \
        dataset.dataset_name=demo_human_or_worm \
        wandb.id=demo_human_or_worm_hyenadna \
        train.pretrained_model_path=path/to/pretrained_model \
        trainer.devices=1

Repeat the experiment

Please see experiment.MD for the details of experiment management. and find scrips in 'experiment' directory

Overview of Model Zoo and Datasets

We support various Genomic foundation models. We are working on add new methods and collecting experiment results.

• Spatiotemporal Prediction Methods.

  Currently supported methods

  • HyenaDNA (NeurIPS'2023)
  • Caduceus (Arxiv'2024)
  • DNABERT (Bioinformatics'2021)
  • DNABERT-2 (Arxiv'2023)
  • The Nucleotide Transformer (BioRxiv'2023)
  • Gena-LM (BioRxiv'2023)

• Genomic foundation models Benchmarks.

  Currently supported datasets

  • Genomic benchmark (BMC Genomic Data'2023) [download] [config]
  • GUE (Arxiv'2023) [download] [config]
  • Promoter prediction (BioRxiv'2023) [download] [config]
  • Splice site prediction (Cell Press'2019) [download] [config]
  • Drosophila enhancer activity prediction (Nature Genetics'2022) [download] [config]
  • Genomic Structure Prediction (Nature Genetics'2022) [download] [config]

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Visualization

We present visualization examples of HyenaDNA below. For more detailed information, please refer to the notebook.

• For species classification task, visualization of t-sne embedding can be found in notebook/gene_cluster.ipynb.

• For visualization of Bulk RNA Expression, please refer to notebook/Bulk_prediction_spearman.ipynb.

• For Genomic Structure Prediction, visualization of predicted structures and ground truth structures are shown in notebook/plot_genomic_structure_h1esc.ipynb and notebook/plot_genomic_structure_hff.ipynb after running the experiment.

• for Drosophila enhancer activity prediction, visualization of predicted enhancers and ground truth enhancers are shown in notebook/drosophila_pearsonr.ipynb after running the experiment.

• for analysis of space complexity, please refer to notebook/count_flops.ipynb and for analysis of length effects and size effects, please refer to notebook/performance_length.ipynb and notebook/parameter_size.ipynb respectively.

License

This project is released under the Apache 2.0 license. See LICENSE for more information.

Acknowledgement

The framework of GenBench is insipred by HyenaDNA

Contact

• Jiahui Li([email protected]), Westlake University
• Zicheng Liu([email protected]), Westlake University
• Lei Xin([email protected]),Westlake University

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