File size: 2,610 Bytes
e0a77a0 cd0a9b4 7b8b89e e0a77a0 7b8b89e cd0a9b4 7b8b89e cd0a9b4 7b8b89e cd0a9b4 7b8b89e b20b374 7b8b89e bab67c3 7b8b89e |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 |
---
library_name: peft
license: mit
language:
- en
tags:
- transformers
- biology
- esm
- esm2
- protein
- protein language model
---
# ESM-2 RNA Binding Site LoRA
This is a Parameter Efficient Fine Tuning (PEFT) Low Rank Adaptation (LoRA) of
the [esm2_t12_35M_UR50D](https://huggingface.co/facebook/esm2_t12_35M_UR50D) model for the (binary) token classification task of
predicting RNA binding sites of proteins. The Github with the training script and conda env YAML can be
[found here](https://github.com/Amelie-Schreiber/esm2_LoRA_binding_sites/tree/main). You can also find a version of this model
that was fine-tuned without LoRA [here](https://huggingface.co/AmelieSchreiber/esm2_t6_8M_UR50D_rna_binding_site_predictor).
## Training procedure
This is a Low Rank Adaptation (LoRA) of `esm2_t6_8M_UR50D`,
trained on `166` protein sequences in the [RNA binding sites dataset](https://huggingface.co/datasets/AmelieSchreiber/data_of_protein-rna_binding_sites)
using a `75/25` train/test split. It achieves an evaluation loss of `0.1791934072971344`.
### Framework versions
- PEFT 0.4.0
## Using the Model
To use, try running:
```python
from transformers import AutoModelForTokenClassification, AutoTokenizer
from peft import PeftModel
import torch
# Path to the saved LoRA model
model_path = "AmelieSchreiber/esm2_t12_35M_LoRA_RNA_binding"
# ESM2 base model
base_model_path = "facebook/esm2_t12_35M_UR50D"
# Load the model
base_model = AutoModelForTokenClassification.from_pretrained(base_model_path)
loaded_model = PeftModel.from_pretrained(base_model, model_path)
# Ensure the model is in evaluation mode
loaded_model.eval()
# Load the tokenizer
loaded_tokenizer = AutoTokenizer.from_pretrained(base_model_path)
# Protein sequence for inference
protein_sequence = "MAVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT" # Replace with your actual sequence
# Tokenize the sequence
inputs = loaded_tokenizer(protein_sequence, return_tensors="pt", truncation=True, max_length=1024, padding='max_length')
# Run the model
with torch.no_grad():
logits = loaded_model(**inputs).logits
# Get predictions
tokens = loaded_tokenizer.convert_ids_to_tokens(inputs["input_ids"][0]) # Convert input ids back to tokens
predictions = torch.argmax(logits, dim=2)
# Define labels
id2label = {
0: "No binding site",
1: "Binding site"
}
# Print the predicted labels for each token
for token, prediction in zip(tokens, predictions[0].numpy()):
if token not in ['<pad>', '<cls>', '<eos>']:
print((token, id2label[prediction]))
```
|