omnigenome 0.3.1a0__tar.gz

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omnigenome-0.3.1a0/PKG-INFO

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+Metadata-Version: 2.4
+Name: omnigenome
+Version: 0.3.1a0
+Summary: OmniGenome: A comprehensive toolkit for genome analysis.
+Home-page: https://github.com/yangheng95/OmniGenBench
+Author: Yang, Heng
+Author-email: hy345@exeter.ac.uk
+License: Apache-2.0
+Platform: Windows
+Platform: Linux
+Platform: Mac OS-X
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: findfile>=2.0.0
+Requires-Dist: autocuda>=0.16
+Requires-Dist: metric-visualizer>=0.9.6
+Requires-Dist: termcolor
+Requires-Dist: gitpython
+Requires-Dist: torch>=2.6.0
+Requires-Dist: pandas
+Requires-Dist: viennarna
+Requires-Dist: scikit-learn
+Requires-Dist: accelerate
+Requires-Dist: transformers>=4.46.0
+Requires-Dist: packaging
+Requires-Dist: peft
+Requires-Dist: dill
+Requires-Dist: accelerate
+Provides-Extra: dev
+Requires-Dist: dill; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+![favicon.png](asset/favicon.png)
+
+<h3 align="center">OmniGenBench is a modular benchmarking platform for evaluating genomic foundation models (GFMs) across diverse tasks like RNA structure prediction, gene function classification, and multi-species generalization.</h3>
+
+<div align="center">
+
+  <a href="https://omnigenbenchdoc.readthedocs.io/en/latest/">
+    <img src="https://img.shields.io/readthedocs/omnigenbench?logo=readthedocs&logoColor=white" alt="Documentation Status" />
+  </a>
+
+  <a href="https://pypi.org/project/omnigenome/">
+    <img src="https://img.shields.io/pypi/v/omnigenome?color=blue&label=PyPI" alt="PyPI" />
+  </a>
+
+  <a href="https://pepy.tech/project/omnigenome">
+    <img src="https://static.pepy.tech/badge/omnigenome" alt="PyPI Downloads" />
+  </a>
+
+  <a href="https://pypi.org/project/omnigenbench/">
+    <img src="https://img.shields.io/pypi/pyversions/omnigenome" alt="Python Version" />
+  </a>
+
+  <a href="https://github.com/yangheng95/omnigenome/blob/main/LICENSE">
+    <img src="https://img.shields.io/github/license/yangheng95/omnigenome" alt="License" />
+  </a>
+
+</div>
+<h3 align="center">
+  <a href="#installation">📦 Installation</a>
+  <span> · </span>
+  <a href="#quick-start">🚀 Getting Started</a>
+  <span> · </span>
+  <a href="#supported-models">🧬 Model Support</a>
+  <span> · </span>
+  <a href="#benchmarks">📊 Benchmarks </a>
+  <span> · </span>
+  <a href="#tutorials">🧪 Application Tutorials</a>
+  <span> · </span>
+  <a href="https://arxiv.org/pdf/2505.14402">📚 Paper</a>
+</h3>
+
+
+## 🔍 What You Can Do with OmniGenBench?
+
+- 🧬 **Benchmark effortlessly** — Run automated and reproducible evaluations for genomic foundation models  
+- 🧠 **Understand your models** — Explore interpretability across diverse tasks and species  
+- ⚙️ **Run tutorials instantly** — Use click-to-run guides for genomic sequence modeling  
+- 🚀 **Train and infer efficiently** — Accelerated workflows for training and inference on GFMs  
+
+## Installation
+
+### Requirements
+Before installing OmniGenome, you need to install the following dependencies:
+- Python 3.10+
+- PyTorch 2.5+
+- Transformers 4.46.0+
+
+### PyPI Installation
+To install OmniGenome, you can use pip:
+```bash
+pip install omnigenome -U
+```
+
+### Source Installation
+Or you can clone the repository and install it from source:
+```bash
+git clone https://github.com/yangheng95/OmniGenBench.git
+cd OmniGenBench
+pip install -e .
+```
+
+## Quick Start
+`OmniGenBench is available for diverse models and benchmark suites, please refer to the  following sections for more details.`
+### Auto-benchmark via CLI
+The following command will download the model from the Hugging Face model hub and run the benchmark on the RGB benchmark:
+```bash
+autobench --model_name_or_path "yangheng/OmniGenome-186M" --benchmark "RGB" --trainer accelerate
+```
+You can find a visualization of AutoBench [here](asset/AutoBench.gif).
+
+
+### Auto-benchmark via Python API
+Or you can use the following python code to run the auto-benchmark:
+```python
+from omnigenome import AutoBench
+gfm = 'LongSafari/hyenadna-medium-160k-seqlen-hf'
+# benchmark could be "RGB", "GB", "PGB", "GUE", which will be downloaded from the Hugging Face model hub
+benchmark = "RGB"
+bench_size = 8
+seeds = [0, 1, 2, 3, 4]
+bench = AutoBench(benchmark=benchmark, model_name_or_path=gfm, overwrite=False)
+bench.run(autocast=False, batch_size=bench_size, seeds=seeds)
+```
+You can find an example of AutoBench via Python API [here](examples/autobench/AutoBench_Tutorial.ipynb).
+
+## Supported Models
+
+
+OmniGenBench provides plug-and-play evaluation for over **30 genomic foundation models**, covering both **RNA** and **DNA** modalities. The following are highlights:
+
+| Model          | Params | Pre-training Corpus                        | Highlights                                          |
+|----------------|--------|--------------------------------------------|-----------------------------------------------------|
+| **OmniGenome** | 186M   | 54B plant RNA+DNA tokens                   | Multi-modal, structure-aware encoder                |
+| **Agro-NT-1B** | 985M   | 48 edible-plant genomes                    | Billion-scale DNA LM w/ NT-V2 k-mer vocab           |
+| **RiNALMo**    | 651M   | 36M ncRNA sequences                        | Largest public RNA LM; FlashAttention-2             |
+| **DNABERT-2**  | 117M   | 32B DNA tokens, 136 species (BPE)          | Byte-pair encoding; 2nd-gen DNA BERT                |
+| **RNA-FM**     | 96M    | 23M ncRNA sequences                        | High performance on RNA structure tasks             |
+| **RNA-MSM**    | 96M    | Multi-sequence alignments                  | MSA-based evolutionary RNA LM                       |
+| **NT-V2**      | 96M    | 300B DNA tokens (850 species)              | Hybrid k-mer vocabulary                             |
+| **HyenaDNA**   | 47M    | Human chromosomes                          | Long-context autoregressive model (1Mb)             |
+| **SpliceBERT** | 19M    | 2M pre-mRNA sequences                      | Fine-grained splice-site recognition                |
+| **Caduceus**   | 1.9M   | Human chromosomes                          | Ultra-compact DNA LM (RC-equivariant)               |
+| **RNA-BERT**   | 0.5M   | 4,000+ ncRNA families                      | Small BERT with nucleotide masking                  |
+| *...and more*  | —      | See Appendix E of the paper                | Includes PlantRNA-FM, UTR-LM, MP-RNA, CALM, etc.    |
+
+## Benchmarks
+
+OmniGenBench supports five curated benchmark suites covering both **sequence-level** and **structure-level** genomics tasks across species.
+
+| Suite        | Focus                       | #Tasks / Datasets        | Sample Tasks                                         |
+|--------------|-----------------------------|--------------------------|------------------------------------------------------|
+| **RGB**      | RNA structure + function    | 12 tasks (SN-level)      | RNA secondary structure, SNMR, degradation prediction |
+| **BEACON**   | RNA (multi-domain)          | 13 tasks                 | Base pairing, mRNA design, RNA contact maps         |
+| **PGB**      | Plant long-range DNA        | 7 categories             | PolyA, enhancer, chromatin access, splice site      |
+| **GUE**      | DNA general tasks           | 36 datasets (9 tasks)    | TF binding, core promoter, enhancer detection       |
+| **GB**       | Classic DNA classification  | 9 datasets               | Human/mouse enhancer, promoter variant classification|
+
+
+## Tutorials
+
+### RNA Design
+RNA design is a fundamental problem in synthetic biology,
+where the goal is to design RNA sequences that fold into a target structure.
+In this demo, we show how to use OmniGenome to design RNA sequences 
+that fold into a target structure using a pre-trained model.
+The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_design/RNA_Design_Tutorial.ipynb).
+
+You can find a visual example of RNA Design [here](asset/RNA_Design.gif).
+
+### RNA Secondary Structure Prediction
+
+RNA secondary structure prediction is a fundamental problem in computational biology,
+where the goal is to predict the secondary structure of an RNA sequence.
+In this demo, we show how to use OmniGenome to predict the secondary structure of RNA sequences using a pre-trained model.
+The tutorials of RNA Secondary Structure Prediction can be found in
+[Secondary_Structure_Prediction_Tutorial.ipynb](examples/rna_secondary_structure_prediction/Secondary_Structure_Prediction_Tutorial.ipynb).
+
+You can find a visual example of RNA Secondary Structure Prediction [here](asset/RNA_Structure_Prediction.gif).
+
+### More Tutorials
+Please find more usage tutorials in [examples/tutorials](examples/tutorials).
+
+## Citation
+```bibtex
+@article{yang2024omnigenbench,
+      title={OmniGenBench: A Modular Platform for Reproducible Genomic Foundation Models Benchmarking}, 
+      author={Heng Yang and Jack Cole, Yuan Li, Renzhi Chen, Geyong Min and Ke Li},
+      year={2024},
+      eprint={https://arxiv.org/abs/2505.14402},
+      archivePrefix={arXiv},
+      primaryClass={q-bio.GN},
+      url={https://arxiv.org/abs/2505.14402}, 
+}
+```
+## License
+OmniGenBench is licensed under the Apache License 2.0. See the LICENSE file for more information.
+
+
+## Contribution
+We welcome contributions to OmniGenBench! If you have any ideas, suggestions, or bug reports, please open an issue or submit a pull request on GitHub.