An Evolutionary-scale Model (ESM) for protein function prediction from amino acid sequences using the Gene Ontology (GO). Based on the ESM2 Transformer architecture, pre-trained on UniRef50, and fine-tuned on the AmiGO dataset, this model predicts the GO subgraph for a particular protein sequence - giving you insight into the molecular function, biological process, and location of the activity inside the cell.

Note: This version only models the biological process subgraph of the gene ontology.

What are GO terms?

"The Gene Ontology (GO) is a concept hierarchy that describes the biological function of genes and gene products at different levels of abstraction (Ashburner et al., 2000). It is a good model to describe the multi-faceted nature of protein function."

"GO is a directed acyclic graph. The nodes in this graph are functional descriptors (terms or classes) connected by relational ties between them (is_a, part_of, etc.). For example, terms 'protein binding activity' and 'binding activity' are related by an is_a relationship; however, the edge in the graph is often reversed to point from binding towards protein binding. This graph contains three subgraphs (subontologies): Molecular Function (MF), Biological Process (BP), and Cellular Component (CC), defined by their root nodes. Biologically, each subgraph represent a different aspect of the protein's function: what it does on a molecular level (MF), which biological processes it participates in (BP) and where in the cell it is located (CC)."

From CAFA 5 Protein Function Prediction

Code Repository

https://github.com/andrewdalpino/esm2-function-classifier

Model Specs

Vocabulary Size: 33
Embedding Dimensions: 480
Attention Heads: 20
Encoder Layers: 12
Context Length: 1026

Basic Example

For a basic demonstration we can rank the GO terms for a particular sequence. For a more advanced example see the predict-subgraph.py source file.

python

import torch

from transformers import EsmTokenizer, EsmForSequenceClassification

model_name = "andrewdalpino/ESM2-35M-Protein-Biological-Process"

tokenizer = EsmTokenizer.from_pretrained(model_name)

model = EsmForSequenceClassification.from_pretrained(model_name)

model.eval()

sequence = "MCNAWYISVDFEKNREDKSKCIHTRRNSGPKLLEHVMYEVLRDWYCLEGENVYMM"

top_k = 10

out = tokenizer(sequence)

input_ids = out["input_ids"]

input_ids = torch.tensor(input_ids, dtype=torch.int64).unsqueeze(0)

with torch.no_grad():
    outputs = model.forward(input_ids)

    probabilities = torch.sigmoid(outputs.logits.squeeze(0))

    probabilities, indices = torch.topk(probabilities, top_k)

probabilities = probabilities.tolist()

terms = [model.config.id2label[index] for index in indices.tolist()]

print(f"Top {args.top_k} GO Terms:")

for term, probability in zip(terms, probabilities):
    print(f"{probability:.4f}: {term}")

References:

A. Rives, et al. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences, 2021.

Z. Lin, et al. Evolutionary-scale prediction of atomic level protein structure with a language model, 2022.

G. A. Merino, et al. Hierarchical deep learning for predicting GO annotations by integrating protein knowledge, 2022.

M. Ashburner, et al. Gene Ontology: tool for the unification of biology, 2000.