Delete README.md
Browse files
README.md
DELETED
|
@@ -1,46 +0,0 @@
|
|
| 1 |
-
---
|
| 2 |
-
license: cc-by-nc-nd-4.0
|
| 3 |
-
---
|
| 4 |
-
|
| 5 |
-
# PepDoRA: A Unified Peptide-Specific Language Model via Weight-Decomposed Low-Rank Adaptation
|
| 6 |
-
|
| 7 |
-
|
| 8 |
-
|
| 9 |
-
In this work, we introduce **PepDoRA**, a SMILES transformer that fine-tunes the state-of-the-art [ChemBERTa-77M-MLM](https://huggingface.co/DeepChem/ChemBERTa-77M-MLM) transformer on modified peptide SMILES via [DoRA](https://nbasyl.github.io/DoRA-project-page/), a novel PEFT method that incorporates weight decomposition. These representations can be leveraged for numerous downstream tasks, including membrane permeability prediction and target binding assessment, for both unmodified and modified peptide sequences.
|
| 10 |
-
|
| 11 |
-
Here's how to extract PepDoRA embeddings for your input peptide:
|
| 12 |
-
|
| 13 |
-
```
|
| 14 |
-
import torch
|
| 15 |
-
from transformers import AutoTokenizer, AutoModel
|
| 16 |
-
|
| 17 |
-
# Load the model and tokenizer
|
| 18 |
-
model_name = "ChatterjeeLab/PepDoRA"
|
| 19 |
-
tokenizer = AutoTokenizer.from_pretrained(model_name)
|
| 20 |
-
model = AutoModel.from_pretrained(model_name, output_hidden_states=True)
|
| 21 |
-
|
| 22 |
-
|
| 23 |
-
# Input peptide sequence
|
| 24 |
-
peptide = "CC(C)C[C@H]1NC(=O)[C@@H](C)NCCCCCCNC(=O)[C@H](CO)NC1=O"
|
| 25 |
-
|
| 26 |
-
# Tokenize the peptide
|
| 27 |
-
inputs = tokenizer(peptide, return_tensors="pt")
|
| 28 |
-
|
| 29 |
-
# Get the hidden states (embeddings) from the model
|
| 30 |
-
with torch.no_grad():
|
| 31 |
-
outputs = model(**inputs,output_hidden_states=True)
|
| 32 |
-
|
| 33 |
-
# Extract the embeddings from the last hidden layer
|
| 34 |
-
embeddng=outputs.last_hidden_state
|
| 35 |
-
|
| 36 |
-
# Print the embedding shape (or the embedding itself)
|
| 37 |
-
print(outputs.last_hidden_state.shape)
|
| 38 |
-
print(embeddng)
|
| 39 |
-
```
|
| 40 |
-
|
| 41 |
-
## Repository Authors
|
| 42 |
-
|
| 43 |
-
[Leyao Wang](mailto:leyao.wang@vanderbilt.edu), Undergraduate Intern in the Chatterjee Lab <br>
|
| 44 |
-
[Pranam Chatterjee](mailto:pranam.chatterjee@duke.edu), Assistant Professor at Duke University
|
| 45 |
-
|
| 46 |
-
Reach out to us with any questions!
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|