README.md

---
tags:
- biology
- ibm
- mammal
- pytorch
- transformers
library_name: mammal
license: apache-2.0
---

## Model Summary

- **Developers:** IBM Research
- **GitHub Repository:** [TBD](TBD)
- **Paper:** [TBD](https://arxiv.org/abs/TBD)
- **Release Date**: Oct ?th, 2024
- **License:** [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0).


## Usage

Using `MAMMAL` requires [TBD](https://github.com/TBD)

```
pip install TBD
```

A simple example:
```python
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: <LINK>


## 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}
}
```