update files and readme
Browse files- README.md +57 -199
- special_tokens_map.json +1 -0
- tokenizer_config.json +15 -0
README.md
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---
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tags:
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## Bias, Risks, and Limitations
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<!-- This section is meant to convey both technical and sociotechnical limitations. -->
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[More Information Needed]
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### Recommendations
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<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
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Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
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## How to Get Started with the Model
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Use the code below to get started with the model.
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[More Information Needed]
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## Training Details
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### Training Data
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<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
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[More Information Needed]
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### Training Procedure
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<!-- This relates heavily to the Technical Specifications. Content here should link to that section when it is relevant to the training procedure. -->
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#### Preprocessing [optional]
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[More Information Needed]
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#### Training Hyperparameters
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- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->
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#### Speeds, Sizes, Times [optional]
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<!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. -->
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[More Information Needed]
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## Evaluation
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<!-- This section describes the evaluation protocols and provides the results. -->
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### Testing Data, Factors & Metrics
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#### Testing Data
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<!-- This should link to a Dataset Card if possible. -->
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[More Information Needed]
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#### Factors
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<!-- These are the things the evaluation is disaggregating by, e.g., subpopulations or domains. -->
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[More Information Needed]
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#### Metrics
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<!-- These are the evaluation metrics being used, ideally with a description of why. -->
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[More Information Needed]
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### Results
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[More Information Needed]
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#### Summary
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## Model Examination [optional]
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<!-- Relevant interpretability work for the model goes here -->
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[More Information Needed]
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## Environmental Impact
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<!-- Total emissions (in grams of CO2eq) and additional considerations, such as electricity usage, go here. Edit the suggested text below accordingly -->
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Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).
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- **Hardware Type:** [More Information Needed]
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- **Hours used:** [More Information Needed]
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- **Cloud Provider:** [More Information Needed]
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- **Compute Region:** [More Information Needed]
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- **Carbon Emitted:** [More Information Needed]
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## Technical Specifications [optional]
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### Model Architecture and Objective
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[More Information Needed]
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### Compute Infrastructure
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[More Information Needed]
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#### Hardware
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[More Information Needed]
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#### Software
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[More Information Needed]
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## Citation [optional]
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<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->
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**BibTeX:**
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[More Information Needed]
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**APA:**
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[More Information Needed]
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## Glossary [optional]
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<!-- If relevant, include terms and calculations in this section that can help readers understand the model or model card. -->
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[More Information Needed]
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## More Information [optional]
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[More Information Needed]
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## Model Card Authors [optional]
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[More Information Needed]
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## Model Card Contact
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[More Information Needed]
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---
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license: apache-2.0
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tags:
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- stripedhyena
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- long context
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- deep signal processing
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- hybrid
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- biology
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- genomics
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---
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## Evo 1.5
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<p align="center">
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<img src="https://cdn-uploads.huggingface.co/production/uploads/62a1306bbe7fa896d2c8de44/JoEHcvLTUlHoMcgh3mmAz.png" width="70%" />
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</p>
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### About
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Evo is a biological foundation model capable of long-context modeling and design.
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Evo uses the [StripedHyena architecture](https://github.com/togethercomputer/stripedhyena) to enable modeling of sequences at a single-nucleotide, byte-level resolution with near-linear scaling of compute and memory relative to context length.
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Evo has 7 billion parameters and is trained on OpenGenome, a prokaryotic whole-genome dataset containing ~300 billion tokens.
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**Evo 1.5** is a version of Evo built off of the Evo 1 model pretrained at 8k context with training extended by 50% more training data, totaling 450 billion tokens.
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| Checkpoint Name | Description |
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|----------------------------------------|-------------|
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| `evo-1.5-8k-base` | A model pretrained with 8,192 context obtained by extending the pretraining of `evo-1-8k-base` to process 50% more training data. |
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| `evo-1-8k-base` | A model pretrained with 8,192 context. We use this model as the base model for molecular-scale finetuning tasks. |
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| `evo-1-131k-base` | A model pretrained with 131,072 context using `evo-1-8k-base` as the initialization. We use this model to reason about and generate sequences at the genome scale. |
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| `evo-1-8k-crispr` | A model fine-tuned on `evo-1-8k-base` specifically on CRISPR-Cas systems. We use this model to generate Cas9/12/13 systems. |
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| `evo-1-8k-transposon` | A model fine-tuned on `evo-1-8k-base` specifically on transposons. We use this to generate IS200/IS605. |
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### How to use Evo
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Example usage is provided in the [standalone repo](https://github.com/evo-design/evo).
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## Cite
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```
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@article{nguyen2024sequence,
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author = {Eric Nguyen and Michael Poli and Matthew G. Durrant and Brian Kang and Dhruva Katrekar and David B. Li and Liam J. Bartie and Armin W. Thomas and Samuel H. King and Garyk Brixi and Jeremy Sullivan and Madelena Y. Ng and Ashley Lewis and Aaron Lou and Stefano Ermon and Stephen A. Baccus and Tina Hernandez-Boussard and Christopher Ré and Patrick D. Hsu and Brian L. Hie },
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title = {Sequence modeling and design from molecular to genome scale with Evo},
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journal = {Science},
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volume = {386},
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number = {6723},
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pages = {eado9336},
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year = {2024},
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doi = {10.1126/science.ado9336},
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URL = {https://www.science.org/doi/abs/10.1126/science.ado9336},
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}
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```
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special_tokens_map.json
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{}
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tokenizer_config.json
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{
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"added_tokens_decoder": {},
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"auto_map": {
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"AutoTokenizer": [
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"tokenizer.ByteTokenizer",
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null
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]
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},
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"byte_level": true,
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"clean_up_tokenization_spaces": true,
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"model_max_length": 1000000000000000019884624838656,
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"padding_side": "left",
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"truncation_side": "left"
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}
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