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CLASP - Contrastive Language-Aminoacid Sequence Pretraining

Repository for creating models pretrained on language and aminoacid sequences similar to ConVIRT, CLIP, and ALIGN.

To dos

1. Finish current big run with preprocessed data (i.e., only preprocessing is the removal of AA length and MW information from the text input with the regex patterns \d+ AA and \d+ MW.)
2. Evaluate the model on zero-shot tasks. See the introduction inference notebook based on the checkpoints from below.

Currently this project is on hold as we don't have the compute to continue the model training.<br> If you want to contribute compute or to extend the project feel free to get in touch (see Discussion below).

Updates

Run 53-54 with UniProt full dataset (~213 mio samples):

Discussion

Alphafold2 discord server, ping @MicPie.

Data

For model training the data provided by UniProt is used.

Requirements

You can install the requirements with the following

$ python setup.py install --user

Then, you must install Microsoft's sparse attention CUDA kernel with the following two steps.

$ sh install_deepspeed.sh

Next, you need to pip install the package triton

$ pip install triton

If both of the above succeeded, now you can train your long biosequences with CLASP

Usage

import torch
from torch.optim import Adam

from clasp import CLASP, Transformer, tokenize

# instantiate the attention models for text and bioseq

text_enc = Transformer(
    num_tokens = 20000,
    dim = 512,
    depth = 6,
    seq_len = 1024,
    reversible = True
)

bioseq_enc = Transformer(
    num_tokens = 21,
    dim = 512,
    depth = 6,
    seq_len = 512,
    sparse_attn = True,
    reversible = True
)

# clasp (CLIP) trainer

clasp = CLASP(
    text_encoder = text_enc,
    bioseq_encoder = bioseq_enc
)

# data

text, text_mask = tokenize(['Spike protein S2: HAMAP-Rule:MF_04099'], context_length = 1024, return_mask = True)

bioseq = torch.randint(0, 21, (1, 511))         # when using sparse attention, should be 1 less than the sequence length
bioseq_mask = torch.ones_like(bioseq).bool()

# do the below with large batch sizes for many many iterations

opt = Adam(clasp.parameters(), lr = 3e-4)

loss = clasp(
    text,
    bioseq,
    text_mask = text_mask,
    bioseq_mask = bioseq_mask,
    return_loss = True               # set return loss to True
)

loss.backward()

Once trained

scores = clasp(
    texts,
    bio_seq,
    text_mask = text_mask,
    bioseq_mask = bioseq_mask
)

Resources

See interesting resources (feel free to add interesting material that could be useful).

Acknowledgements

This project is supported by EleutherAI.

Citations

@article{zhang2020contrastive,
  title={Contrastive learning of medical visual representations from paired images and text},
  author={Zhang, Yuhao and Jiang, Hang and Miura, Yasuhide and Manning, Christopher D and Langlotz, Curtis P},
  journal={arXiv preprint arXiv:2010.00747},
  year={2020}
}

OpenAI blog post "CLIP: Connecting Text and Images"

@article{radford2021learning,
  title={Learning transferable visual models from natural language supervision},
  author={Radford, Alec and Kim, Jong Wook and Hallacy, Chris and Ramesh, Aditya and Goh, Gabriel and Agarwal, Sandhini and Sastry, Girish and Askell, Amanda and Mishkin, Pamela and Clark, Jack and others},
  journal={arXiv preprint arXiv:2103.00020},
  year={2021}
}

@article{jia2021scaling,
  title={Scaling Up Visual and Vision-Language Representation Learning With Noisy Text Supervision},
  author={Jia, Chao and Yang, Yinfei and Xia, Ye and Chen, Yi-Ting and Parekh, Zarana and Pham, Hieu and Le, Quoc V and Sung, Yunhsuan and Li, Zhen and Duerig, Tom},
  journal={arXiv preprint arXiv:2102.05918},
  year={2021}
}