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CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer

This repository is the official implementation of CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer.

Requirements

Create a virtual environment and install the required packages via:

pip install -r requirements.txt

Next, install torch = 2.0.0 with the appropriate CUDA version

Model Downloads

Models are available on Hugging Face.

We also have two spaces available where you can run predictions on your own data!

• Image Prediction
• Sequence Prediction

Generating Images

To generate images, set the saved model as the ckpt_path. This method can be unstable, so refer to Demo.ipynb to see another way of loading.

from omegaconf import OmegaConf
from celle_main import instantiate_from_config

configs = OmegaConf.load(configs/celle.yaml);

model = instantiate_from_config(configs.model).to(device);

model.sample(text=sequence,
                      condition=nucleus,
                      return_logits=True,
                      progress=True)

Sequence Prediction

model.sample_text(condition=nucleus,
                  image=image,
                  return_logits=True,
                  progress=True)

Training

Training for CELL-E occurs in 3 stages:

• Training Protein Threshold Image Encoder
• Training a Nucleus Image Encoder
• Training CELL-E Transformer

VQGANs

If using the protein threshold image, set threshold: True for the dataset.

We use a slightly modified version of the taming-transformers code.

To train, run the following script:

python celle_taming_main.py --base configs/threshold_vqgan.yaml -t True

Please refer to the original repo for additional flags, such as --gpus.

Preparing Dataset

Images

We provide scripts for downloading Human Protein Atlas and OpenCell images in the scripts folder. A data_csv is needed to for the dataloader. You must generate a csv file which contains the columns nucleus_image_path, protein_image_path, metadata_path, split (train or val), and sequence (optional). It is assumed that this file exists within the the same general data folder as the images and metadata files.

Metadata

Metadata is a JSON which should accompany every protein sequence. If a sequence does not appear in the data_csv, it must appear in metadata.json with the a key named protein_sequence.

Adding more information here can be useful for querying individual proteins. They can be retrieved via retrieve_metadata, which creates a self.metadata variable within the dataset object.

To train, run the following script:

python celle_main.py --base configs/celle.yaml -t True

Specify --gpus in the same format as VQGAN.

CELL-E contains the following options:

• ckpt_path : Resume previous CELL-E 2 training. Saved model with state_dict
• vqgan_model_path : Saved protein image model (with state_dict) for protein image encoder
• vqgan_config_path: Saved protein image model yaml
• condition_model_path : Saved condition (nucleus) model (with state_dict) for protein image encoder
• condition_config_path: Saved condition (nucleus) model yaml
• num_images: 1 if only using protein image encoder, 2 if including condition image encoder
• image_key: nucleus, target, or threshold
• dim: Dimension of language model embedding
• num_text_tokens: total number of tokens in language model (33 for ESM-2)
• text_seq_len: Total number of amino acids considered
• depth: Transformer model depth, deeper is usually better at the cost of VRAM
• heads: number of heads used in multi-headed attention
• dim_head: size of attention heads
• attn_dropout: Attention Dropout rate in training
• ff_dropout: Feed-Forward Dropout rate in training
• loss_img_weight: Weighting applied to image reconstruction. text weight = 1
• loss_text_weight: Weighting applied to condition image reconstruction.
• stable: Norms weights (for when exploding gradients occur)
• learning_rate: Learning rate for Adam optimizer
• monitor: Param used to save models

Citation

Please cite us if you decide to use our code for any part of your research.

@inproceedings{
anonymous2023translating,
title={CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer},
author={Emaad Khwaja, Yun S. Song, Aaron Agarunov, and Bo Huang},
booktitle={Thirty-seventh Conference on Neural Information Processing Systems},
year={2023},
url={https://openreview.net/forum?id=YSMLVffl5u}
}