license: mit
language:
- en
library_name: transformers
tags:
- ems
- esm2
- biology
- protein
- protein language model
- cafa 5
- protein function prediction
ESM-2 for Protein Function Prediction
This model is not intended for protein function prediction, but rather as a checkpoint for further fine-tuning, especially
with Low Rank Adaptation (LoRA). This is an experimental model fine-tuned from the
esm2_t6_8M_UR50D model
for multi-label classification. In particular, the model is fine-tuned on the CAFA-5 protein sequence dataset available
here. More precisely, the train_sequences.fasta file is the
list of protein sequences that were trained on, and the
train_terms.tsv file contains the gene ontology protein function labels for each protein sequence. For more details on using
ESM-2 models for multi-label sequence classification, see here.
Due to the potentially complicated class weighting necessary for the hierarchical ontology, further fine-tuning will be necessary.
Fine-Tuning
The model was fine-tuned for 7 epochs at a learning rate of 5e-5, and achieves the following metrics:
Validation Loss: 0.0027,
Validation Micro F1: 0.3672,
Validation Macro F1: 0.9967,
Validation Micro Precision: 0.6052,
Validation Macro Precision: 0.9996,
Validation Micro Recall: 0.2626,
Validation Macro Recall: 0.9966
Using the model
First, downlowd the file go-basic.obo from here
and store the file locally, then provide the local path in the the code below:
import torch
from transformers import AutoTokenizer, EsmForSequenceClassification
from sklearn.metrics import precision_recall_fscore_support
# 1. Parsing the go-basic.obo file
def parse_obo_file(file_path):
with open(file_path, 'r') as f:
data = f.read().split("[Term]")
terms = []
for entry in data[1:]:
lines = entry.strip().split("\n")
term = {}
for line in lines:
if line.startswith("id:"):
term["id"] = line.split("id:")[1].strip()
elif line.startswith("name:"):
term["name"] = line.split("name:")[1].strip()
elif line.startswith("namespace:"):
term["namespace"] = line.split("namespace:")[1].strip()
elif line.startswith("def:"):
term["definition"] = line.split("def:")[1].split('"')[1]
terms.append(term)
return terms
parsed_terms = parse_obo_file("go-basic.obo") # Replace `go-basic.obo` with your path
# 2. Load the saved model and tokenizer
model_path = "AmelieSchreiber/cafa_5_protein_function_prediction"
loaded_model = EsmForSequenceClassification.from_pretrained(model_path)
loaded_tokenizer = AutoTokenizer.from_pretrained(model_path)
# 3. The predict_protein_function function
def predict_protein_function(sequence, model, tokenizer, go_terms):
inputs = tokenizer(sequence, return_tensors="pt", padding=True, truncation=True, max_length=1022)
model.eval()
with torch.no_grad():
outputs = model(**inputs)
predictions = torch.sigmoid(outputs.logits)
predicted_indices = torch.where(predictions > 0.05)[1].tolist()
functions = []
for idx in predicted_indices:
term_id = unique_terms[idx] # Use the unique_terms list from your training script
for term in go_terms:
if term["id"] == term_id:
functions.append(term["name"])
break
return functions
# 4. Predicting protein function for an example sequence
example_sequence = "MAYLGSLVQRRLELASGDRLEASLGVGSELDVRGDRVKAVGSLDLEEGRLEQAGVSMA" # Replace with your protein sequence
predicted_functions = predict_protein_function(example_sequence, loaded_model, loaded_tokenizer, parsed_terms)
print(predicted_functions)