Introduction

Dataset DOI: 10.5061/dryad.m905qfv9p

Huggingface repo

FAPM Demo

Installation

1. (Optional) Creating conda environment

conda create -n lavis python=3.8
conda activate lavis

2. for development, you may build from source

git clone https://github.com/xiangwenkai/FAPM.git
cd FAPM
pip install -e .

# if needed
# pip install Biopython
# pip install fair-esm

Datasets

1.raw dataset

Raw data are avaliable at https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2023_04/knowledgebase/, this file is very large and need to be processed to get its name, sequence, GO label, function description and prompt.
The domain level protein dataset we used are avaliable at https://ftp.ebi.ac.uk/pub/databases/interpro/releases/95.0/protein2ipr.dat.gz
In this respository, We provide the experimental train/val/test sets of Swiss-Prot, which are avaliable at data/swissprot_exp

2.ESM2 embeddings

Source code for ESM2 embeddings generation: https://github.com/facebookresearch/esm
The generation command:

conda activate FAPM
python esm_scripts/extract.py esm2_t36_3B_UR50D you_path/protein.fasta you_path_to_save_embedding_files --repr_layers 36 --truncation_seq_length 1024 --include per_tok

Example:

conda activate FAPM
python esm_scripts/extract.py esm2_t36_3B_UR50D data/fasta/example.fasta data/emb_esm2_3b --repr_layers 36 --truncation_seq_length 1024 --include per_tok

The default path to save embedding files is data/emb_esm2_3b You can refer to data/fasta/prepare_custom_fasta.py to prepare your custom fasta data.

Pretraining language models

Source: https://huggingface.co/teknium/OpenHermes-2.5-Mistral-7B

Training

data config: lavis/configs/datasets/protein/GO_defaults_cap.yaml
stage1 config: lavis/projects/blip2/train/protein_pretrain_stage1.yaml
stage1 training command: run_scripts/blip2/train/protein_pretrain_domain_stage1.sh
stage2 config: lavis/projects/blip2/train/protein_pretrain_stage2.yaml
stage2 training/finetuning command: run_scripts/blip2/train/protein_pretrain_domain_stage2.sh

Trained models

The models are avaliable at https://huggingface.co/wenkai/FAPM/tree/main/model
You can also download our trained models from google drive: https://drive.google.com/drive/folders/1aA0eSYxNw3DvrU5GU1Cu-4q2kIxxAGSE?usp=drive_link

Testing

config: lavis/projects/blip2/eval/caption_protein_eval.yaml
command: run_scripts/blip2/eval/eval_cap_protein.sh

Inference example

python FAPM_inference.py \
--model_path model/checkpoint_mf2.pth \
--example_path data/emb_esm2_3b/P18281.pt \
--device cuda \
--prompt Acanthamoeba \
--prop True