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README.md
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@@ -43,7 +43,7 @@ model = AutoModelForMaskedLM.from_pretrained('Synthyra/ESMplusplus_small', trust
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```
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## Embed entire datasets with no new code
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To embed a list of protein sequences **fast**, just call embed_dataset. Sequences are sorted to reduce padding tokens, so the progress bar is usually much longer than the actual time.
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```python
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embeddings = model.embed_dataset(
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sequences=sequences, # list of protein strings
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## Inference speeds
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We look at various ESM models and their throughput on an H100. Adding efficient batching between ESMC and ESM++ significantly improves the throughput. ESM++ small is even faster than ESM2-35M with long sequences!
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The most gains will be seen with PyTorch > 2.5 on linux machines.
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![image/png](https://cdn-uploads.huggingface.co/production/uploads/62f2bd3bdb7cbd214b658c48/
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### Citation
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If you use any of this implementation or work please cite it (as well as the ESMC preprint). Bibtex for both coming soon.
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```
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## Embed entire datasets with no new code
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+
To embed a list of protein sequences **fast**, just call embed_dataset. Sequences are sorted to reduce padding tokens, so the initial progress bar estimation is usually much longer than the actual time.
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```python
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embeddings = model.embed_dataset(
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sequences=sequences, # list of protein strings
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## Inference speeds
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We look at various ESM models and their throughput on an H100. Adding efficient batching between ESMC and ESM++ significantly improves the throughput. ESM++ small is even faster than ESM2-35M with long sequences!
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The most gains will be seen with PyTorch > 2.5 on linux machines.
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+
![image/png](https://cdn-uploads.huggingface.co/production/uploads/62f2bd3bdb7cbd214b658c48/aqe1nozNdwaL0bgaUKBPp.png)
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### Citation
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If you use any of this implementation or work please cite it (as well as the ESMC preprint). Bibtex for both coming soon.
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