ibm/biomed.omics.bl.sm.ma-ted-400m

Model Summary

MAMMAL (Molecular Aliened Multi-Modal Architect Language), a versatile multi-task foundation model that learns from large-scale biological datasets (over 2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a query syntax that supports a wide range of tasks such as classification, regression, and generation—by combining different modalities and entity types as inputs and/or outputs.

• Developers: IBM Research
• GitHub Repository: TBD
• Paper: TBD
• Release Date: Oct ?th, 2024
• License: Apache 2.0.

Usage

Using MAMMAL requires TBD

pip install TBD

A simple example:

import torch
from fuse.data.tokenizers.modular_tokenizer.op import ModularTokenizerOp
from mammal.model import Mammal
from mammal.keys import *

# Load Model
model = Mammal.from_pretrained("ibm/biomed.omics.bl.sm.ma-ted-400m")

# Load Tokenizer
tokenizer_op = ModularTokenizerOp.from_pretrained("ibm/biomed.omics.bl.sm.ma-ted-400m")

# Prepare Input Prompt
protein_calmodulin = "MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMISELDQDGFIDKEDLHDGDGKISFEEFLNLVNKEMTADVDGDGQVNYEEFVTMMTSK"
protein_calcineurin = "MSSKLLLAGLDIERVLAEKNFYKEWDTWIIEAMNVGDEEVDRIKEFKEDEIFEEAKTLGTAEMQEYKKQKLEEAIEGAFDIFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIRQMWDQNGDWDRIKELKFGEIKKLSAKDTRGTIFIKVFENLGTGVDSEYEDVSKYMLKHQ"

# Create and load sample
sample_dict = dict()
# Formatting prompt to match pre-training syntax
sample_dict[ENCODER_INPUTS_STR] = f"<@TOKENIZER-TYPE=AA><BINDING_AFFINITY_CLASS><SENTINEL_ID_0><MOLECULAR_ENTITY><MOLECULAR_ENTITY_GENERAL_PROTEIN><SEQUENCE_NATURAL_START>{protein_calmodulin}<SEQUENCE_NATURAL_END><MOLECULAR_ENTITY><MOLECULAR_ENTITY_GENERAL_PROTEIN><SEQUENCE_NATURAL_START>{protein_calcineurin}<SEQUENCE_NATURAL_END><EOS>"

# Tokenize
tokenizer_op(
    sample_dict=sample_dict,
    key_in=ENCODER_INPUTS_STR,
    key_out_tokens_ids=ENCODER_INPUTS_TOKENS,
    key_out_attention_mask=ENCODER_INPUTS_ATTENTION_MASK,
)
sample_dict[ENCODER_INPUTS_TOKENS] = torch.tensor(sample_dict[ENCODER_INPUTS_TOKENS])
sample_dict[ENCODER_INPUTS_ATTENTION_MASK] = torch.tensor(sample_dict[ENCODER_INPUTS_ATTENTION_MASK])

# Generate Prediction
batch_dict = model.generate(
    [sample_dict],
    output_scores=True,
    return_dict_in_generate=True,
    max_new_tokens=5,
)

# Get output
generated_output = tokenizer_op._tokenizer.decode(batch_dict[CLS_PRED][0])
print(f"{generated_output=}")

For more advanced usage, see our detailed example at:

Citation

If you found our work useful, please consider to give a star to the repo and cite our paper:

@article{TBD,
  title={TBD},
  author={IBM Research Team},
  jounal={arXiv preprint arXiv:TBD},
  year={2024}
}