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--- |
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tags: |
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- biology |
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- small-molecule |
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- single-cell-genes |
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- drug-discovery |
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- ibm |
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- mammal |
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- pytorch |
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library_name: biomed |
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license: apache-2.0 |
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--- |
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The **ibm/biomed.omics.bl.sm.ma-ted-458m** model is a biomedical foundation model trained on over 2 billion biological samples across multiple modalities, including proteins, small molecules, and single-cell gene data. |
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Designed for robust performance, it achieves state-of-the-art results over a variety of tasks across the entire drug discovery pipeline and the diverse biomedical domains. |
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Based on the **M**olecular **A**ligned **M**ulti-**M**odal **A**rchitecture and **L**anguage (**MAMMAL**), a flexible, multi-domain architecture with an adaptable task prompt syntax. |
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The syntax allows for dynamic combinations of tokens and scalars, enabling classification, regression, and generation tasks either within a single domain or with cross-domain entities. |
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## Model Summary |
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- **Developers:** IBM Research |
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- **GitHub Repository:** https://github.com/BiomedSciAI/biomed-multi-alignment |
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- **Paper:** https://arxiv.org/abs/2410.22367 |
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- **Release Date**: Oct 28th, 2024 |
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- **License:** [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0). |
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## Usage |
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Using `ibm/biomed.omics.bl.sm.ma-ted-458m` requires installing https://github.com/BiomedSciAI/biomed-multi-alignment |
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``` |
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pip install git+https://github.com/BiomedSciAI/biomed-multi-alignment.git |
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``` |
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A simple example for a task already supported by `ibm/biomed.omics.bl.sm.ma-ted-458m`: |
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```python |
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import torch |
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from fuse.data.tokenizers.modular_tokenizer.op import ModularTokenizerOp |
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from mammal.model import Mammal |
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from mammal.keys import * |
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# Load Model |
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model = Mammal.from_pretrained("ibm/biomed.omics.bl.sm.ma-ted-458m") |
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model.eval() |
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# Load Tokenizer |
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tokenizer_op = ModularTokenizerOp.from_pretrained("ibm/biomed.omics.bl.sm.ma-ted-458m") |
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# Prepare Input Prompt |
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protein_calmodulin = "MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMISELDQDGFIDKEDLHDGDGKISFEEFLNLVNKEMTADVDGDGQVNYEEFVTMMTSK" |
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protein_calcineurin = "MSSKLLLAGLDIERVLAEKNFYKEWDTWIIEAMNVGDEEVDRIKEFKEDEIFEEAKTLGTAEMQEYKKQKLEEAIEGAFDIFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIRQMWDQNGDWDRIKELKFGEIKKLSAKDTRGTIFIKVFENLGTGVDSEYEDVSKYMLKHQ" |
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# Create and load sample |
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sample_dict = dict() |
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# Formatting prompt to match pre-training syntax |
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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>" |
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# Tokenize |
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tokenizer_op( |
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sample_dict=sample_dict, |
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key_in=ENCODER_INPUTS_STR, |
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key_out_tokens_ids=ENCODER_INPUTS_TOKENS, |
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key_out_attention_mask=ENCODER_INPUTS_ATTENTION_MASK, |
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) |
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sample_dict[ENCODER_INPUTS_TOKENS] = torch.tensor(sample_dict[ENCODER_INPUTS_TOKENS]) |
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sample_dict[ENCODER_INPUTS_ATTENTION_MASK] = torch.tensor(sample_dict[ENCODER_INPUTS_ATTENTION_MASK]) |
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# Generate Prediction |
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batch_dict = model.generate( |
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[sample_dict], |
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output_scores=True, |
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return_dict_in_generate=True, |
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max_new_tokens=5, |
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) |
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# Get output |
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generated_output = tokenizer_op._tokenizer.decode(batch_dict[CLS_PRED][0]) |
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print(f"{generated_output=}") |
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``` |
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For more advanced usage, see our detailed example at: <LINK> |
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## Citation |
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If you found our work useful, please consider to give a star to the repo and cite our paper: |
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``` |
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@misc{shoshan2024mammalmolecularaligned, |
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title={MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language}, |
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author={Yoel Shoshan and Moshiko Raboh and Michal Ozery-Flato and Vadim Ratner and Alex Golts and Jeffrey K. Weber and Ella Barkan and Simona Rabinovici-Cohen and Sagi Polaczek and Ido Amos and Ben Shapira and Liam Hazan and Matan Ninio and Sivan Ravid and Michael M. Danziger and Joseph A. Morrone and Parthasarathy Suryanarayanan and Michal Rosen-Zvi and Efrat Hexter}, |
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year={2024}, |
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eprint={2410.22367}, |
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archivePrefix={arXiv}, |
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primaryClass={q-bio.QM}, |
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url={https://arxiv.org/abs/2410.22367}, |
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} |
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``` |
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