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OntoProtein

This is the implement of the ICLR2022 paper "OntoProtein: Protein Pretraining With Ontology Embedding". OntoProtein is an effective method that make use of structure in GO (Gene Ontology) into text-enhanced protein pre-training model.

• ❗NOTE: We provide a NLP for science paper-list at https://github.com/zjunlp/NLP4Science_Papers.

Quick links

• Overview
• Requirements
  • Environment for pre-training data generation
  • Environmen for OntoProtein pre-training
  • Environment for protein-related tasks
• Data preparation
  • Pre-training data
  • Downstream task data
• Protein pre-training model
• Usage for protein-related tasks
• Citation

Overview

<span id="overview"></span>

In this work we present OntoProtein, a knowledge-enhanced protein language model that jointly optimize the KE and MLM objectives, which bring excellent improvements to a wide range of protein tasks. And we introduce ProteinKG25, a new large-scale KG dataset, promting the research on protein language pre-training.

Requirements

<span id="requirements"></span> To run our code, please install dependency packages for related steps.

Environment for pre-training data generation

<span id="environment-for-pre-training-data-generation"></span> python3.8 / biopython 1.37 / goatools

For extracting the definition of the GO term, we motified the code in goatools library. The changes in goatools.obo_parser are as follows:

# line 132
elif line[:5] == "def: ":
    rec_curr.definition = line[5:]

# line 169
self.definition = ""

Environment for OntoProtein pre-training

<span id="environment-for-ontoprotein-pre-training"></span> python3.8 / pytorch 1.9 / transformer 4.5.1+ / deepspeed 0.5.1/ lmdb /

Environment for protein-related tasks

<span id="environment-for-protein-related-tasks"></span> python3.8 / pytorch 1.9 / transformer 4.5.1+ / lmdb / tape_proteins

Specially, in library tape_proteins, it only implements the calculation of metric P@L for the contact prediction task. So, for reporting the metrics P@K taking different K values, in which the metrics P@K are precisions for the top K contacts, we made some changes in the library. Detailed changes could be seen in [isssue #8]

Note: environments configurations of some baseline models or methods in our experiments, e.g. BLAST, DeepGraphGO, we provide related links to configurate as follows:

BLAST / Interproscan / DeepGraphGO / GNN-PPI

Data preparation

<span id="data-preparation"></span> For pretraining OntoProtein, fine-tuning on protein-related tasks and inference, we provide acquirement approach of related data.

Pre-training data

<span id="pre-training-data"></span> To incorporate Gene Ontology knowledge into language models and train OntoProtein, we construct ProteinKG25, a large-scale KG dataset with aligned descriptions and protein sequences respectively to GO terms and protein entities. There have two approach to acquire the pre-training data: 1) download our prepared data ProteinKG25, 2) generate your own pre-training data.

Download released data

We have released our prepared data ProteinKG25 in Google Drive.

The whole compressed package includes following files:

• go_def.txt: GO term definition, which is text data. We concatenate GO term name and corresponding definition by colon.
• go_type.txt: The ontology type which the specific GO term belong to. The index is correponding to GO ID in go2id.txt file.
• go2id.txt: The ID mapping of GO terms.
• go_go_triplet.txt: GO-GO triplet data. The triplet data constitutes the interior structure of Gene Ontology. The data format is < h r t>, where h and t are respectively head entity and tail entity, both GO term nodes. r is relation between two GO terms, e.g. is_a and part_of.
• protein_seq.txt: Protein sequence data. The whole protein sequence data are used as inputs in MLM module and protein representations in KE module.
• protein2id.txt: The ID mapping of proteins.
• protein_go_train_triplet.txt: Protein-GO triplet data. The triplet data constitutes the exterior structure of Gene Ontology, i.e. Gene annotation. The data format is <h r t>, where h and t are respectively head entity and tail entity. It is different from GO-GO triplet that a triplet in Protein-GO triplet means a specific gene annotation, where the head entity is a specific protein and tail entity is the corresponding GO term, e.g. protein binding function. r is relation between the protein and GO term.
• relation2id.txt: The ID mapping of relations. We mix relations in two triplet relation.

Generate your own pre-training data

For generating your own pre-training data, you need download following raw data:

• go.obo: the structure data of Gene Ontology. The download link and detailed format see in Gene Ontology`
• uniprot_sprot.dat: protein Swiss-Prot database. [link]
• goa_uniprot_all.gaf: Gene Annotation data. [link]

When download these raw data, you can excute following script to generate pre-training data:

python tools/gen_onto_protein_data.py

Downstream task data

<span id="downstream-task-data"></span> Our experiments involved with several protein-related downstream tasks. [Download datasets]

Protein pre-training model

<span id="protein-pre-training-model"></span> You can pre-training your own OntoProtein based above pretraining dataset. Before pretraining OntoProtein, you need to download two pretrained model, respectively ProtBERT and PubMedBERT and save them in data/model_data/ProtBERT and data/model_data/PubMedBERT. We provide the script bash script/run_pretrain.sh to run pre-training. And the detailed arguments are all listed in src/training_args.py, you can set pre-training hyperparameters to your need.

Usage for protein-related tasks

<span id="usage-for-protein-related-tasks"></span>

We have released the checkpoint of pretrained model on the model library of Hugging Face. [Download model].

Running examples

The shell files of training and evaluation for every task are provided in script/ , and could directly run. Also, you can utilize the running codes run_downstream.py , and write your shell files according to your need:

• run_downstream.py: support {ss3, ss8, contact, remote_homology, fluorescence, stability} tasks;

Training models

Running shell files: bash script/run_{task}.sh, and the contents of shell files are as follow:

bash run_main.sh \
    --model model_data/ProtBertModel \
    --output_file ss3-ProtBert \
    --task_name ss3 \
    --do_train True \
    --epoch 5 \
    --optimizer AdamW \
    --per_device_batch_size 2 \
    --gradient_accumulation_steps 8 \
    --eval_step 100 \
    --eval_batchsize 4 \
    --warmup_ratio 0.08 \
    --frozen_bert False

Arguments for the training and evalution script are as follows,

• --task_name: Specify which task to evaluate on, and now the script supports {ss3, ss8, contact, remote_homology, fluorescence, stability} tasks;
• --model: The name or path of a protein pre-trained checkpoint.
• --output_file: The path of the fine-tuned checkpoint saved.
• --do_train: Specify if you want to finetune the pretrained model on downstream tasks.
• --epoch: Epochs for training model.
• --optimizer: The optimizer to use, e.g., AdamW.
• --per_device_batch_size: Batch size per GPU.
• --gradient_accumulation_steps: The number of gradient accumulation steps.
• --warmup_ratio: Ratio of total training steps used for a linear warmup from 0 to learning_rate.
• --frozen_bert: Specify if you want to frozen the encoder in the pretrained model.

Additionally, you can set more detailed parameters in run_main.sh.

Notice: the best checkpoint is saved in OUTPUT_DIR/.

How to Cite

@inproceedings{
zhang2022ontoprotein,
title={OntoProtein: Protein Pretraining With Gene Ontology Embedding},
author={Ningyu Zhang and Zhen Bi and Xiaozhuan Liang and Siyuan Cheng and Haosen Hong and Shumin Deng and Qiang Zhang and Jiazhang Lian and Huajun Chen},
booktitle={International Conference on Learning Representations},
year={2022},
url={https://openreview.net/forum?id=yfe1VMYAXa4}
}