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CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction

This repository is the official implementation of CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction.

schematic

Requirements

Create a virtual environment and install the required packages via:

pip install -r requirements.txt

Next, install torch = 1.7.1 and torchvision==0.8.2 with the appropriate CUDA version

Preparing Dataset

Images

We used OpenCell for CELL-E, which has information on downloading the entire dataset. 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, and split (train or val). 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.

Training

Training for CELL-E occurs in 2 (or 3) stages:

  • Training Protein Threshold Image encoder
  • (Optional, but recommended) Training a Nucleus Image (Conditional Image) Encoder
  • Training CELL-E Transformer

Image Encoders

There are two available image encoders in this repository: Discrete VAE (Similar to the original OpenAI implementation) and VQGAN (recommended). If using the protein threshold image, set threshold: True for the dataset.

Discrete VAE

The discrete VAE can be trained using the following code:

from celle import DiscreteVAE

vae = DiscreteVAE(
    image_size = 256,
    num_layers = 3,           # number of downsamples - ex. 256 / (2 ** 3) = (32 x 32 feature map)
    channels = 1,
    num_tokens = 512,        # number of visual tokens. in the paper, they used 8192, but could be smaller for downsized projects
    codebook_dim = 512,       # codebook dimension
    hidden_dim = 64,          # hidden dimension
    num_resnet_blocks = 1,    # number of resnet blocks
    temperature = 0.9,        # gumbel softmax temperature, the lower this is, the harder the discretization
    straight_through = False, # straight-through for gumbel softmax. unclear if it is better one way or the other)

loss = vae(images, return_loss = True)
loss.backward()

VQGAN (Recommended)

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.

CELL-E

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 from dalle-pytorch.

  • ckpt_path : Resume previous CELL-E 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 : (Optional) Saved condition (nucleus) model (with state_dict) for protein image encoder

  • condition_config_path: (Optional) 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 (768 for BERT)

  • num_text_tokens: total number of tokens in language model (30 for BERT)

  • 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

  • reversible: See https://github.com/lucidrains/DALLE-pytorch#scaling-depth

  • attn_dropout: Attention Dropout rate in training

  • ff_dropout: Feed-Forward Dropout rate in training

  • attn_types: See https://github.com/lucidrains/DALLE-pytorch#sparse-attention. Sparse attention not supported

  • loss_img_weight: Weighting applied to image reconstruction. text weight = 1

  • loss_cond_weight: Weighting applied to condition image reconstruction.

  • stable: Norms weights (for when exploding gradients occur)

  • sandwich_norm: See https://github.com/lucidrains/x-transformers#sandwich-norm

  • shift_tokens: Applies shift in feature dimension. Only applied to images.

  • rotary_emb: Rotary embedding scheme for positional encoding

  • text_embedding: language used for model. no_text, unirep, bert, esm1b, onehot, aadescriptors available

  • fixed_embedding: Setting to True allows for protein sequence embeddings to be updated during training

  • learning_rate: Learning rate for Adam optimizer

  • monitor: Param used to save models

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.

import OmegaConf
from celle_main import instantiate_from_config

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

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

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

Citation

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

CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction
Emaad Khwaja, Yun S. Song, Bo Huang
bioRxiv 2022.05.27.493774; doi: https://doi.org/10.1101/2022.05.27.493774

Acknowledgements

Huge shoutout to @lucidrains for putting out dalle-pytorch, which this code is based on. This work would not have been possible without the invaluable contribution.