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--- |
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tags: |
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- molecular language model |
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- SELFIES |
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- molecule optimization |
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inference: false |
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--- |
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# MolGen-large-opt |
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MolGen-large-opt was introduced in the paper ["Domain-Agnostic Molecular Generation with Self-feedback"](https://arxiv.org/pdf/2301.11259.pdf) and first released in [this repository](https://github.com/zjunlp/MolGen). |
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## Model description |
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MolGen-large-opt is the fine-tuned version of [MolGen-large](https://huggingface.co/zjunlp/MolGen-large). MolGen-large is the first pre-trained model that only produces chemically valid molecules. |
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With a training corpus of over 100 million molecules in SELFIES representation, MolGen-large learns the intrinsic structural patterns of molecules by mapping corrupted SELFIES to their original forms. |
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Specifically, MolGen-large employs a bidirectional Transformer as its encoder and an autoregressive Transformer as its decoder. |
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Through its carefully designed multi-task molecular prefix tuning (MPT), MolGen-large-opt can generate molecules with desired properties, making it a valuable tool for molecular optimization. |
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## Intended uses |
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You can use the fine-tuned model for molecule optimization for downstream tasks. See the [repository](https://github.com/zjunlp/MolGen) to look for fine-tune details on a task that interests you. |
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### How to use |
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Molecule optimization example: |
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```python |
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>>> from transformers import AutoTokenizer, AutoModelForSeq2SeqLM |
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>>> tokenizer = AutoTokenizer.from_pretrained("zjunlp/MolGen-large-opt") |
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>>> model = AutoModelForSeq2SeqLM.from_pretrained("zjunlp/MolGen-large-opt") |
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>>> sf_input = tokenizer("[N][#C][C][C][C@@H1][C][C][C][C][C][C][C][C][C][C][C][Ring1][N][=O]", return_tensors="pt") |
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>>> # beam search |
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>>> molecules = model.generate(input_ids=sf_input["input_ids"], |
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attention_mask=sf_input["attention_mask"], |
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max_length=35, |
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min_length=5, |
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num_return_sequences=5, |
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num_beams=5) |
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>>> sf_output = [tokenizer.decode(g, skip_special_tokens=True, clean_up_tokenization_spaces=True).replace(" ","") for g in molecules] |
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['[N][#C][C][C][C@@H1][C][C][C][C][C][C][C][C][C][C][C][C][Ring1][N][=O]', |
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'[N][#C][C][C][C@@H1][C][C][C][C][C][C][C][C][C][C][C][Ring1][N][=O]', |
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'[N][#C][C][C][C@@H1][C][C][C][C][C][C][C][C][C][C][C][C][C][Ring1][N][=O]', |
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'[N][#C][C][C][C@@H1][C][C][C][C][C][C][C][C][C][C][Ring1][N][=O]', |
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'[N][#C][C][C][C@@H1][C][C][C][C][C][C][C][C][C][C][C][C][C][C][Ring1][N][=O]'] |
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``` |
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### BibTeX entry and citation info |
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```bibtex |
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@inproceedings{fang2023domain, |
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author = {Yin Fang and |
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Ningyu Zhang and |
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Zhuo Chen and |
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Xiaohui Fan and |
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Huajun Chen}, |
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title = {Domain-Agnostic Molecular Generation with Chemical Feedback}, |
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booktitle = {{ICLR}}, |
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publisher = {OpenReview.net}, |
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year = {2024}, |
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url = {https://openreview.net/pdf?id=9rPyHyjfwP} |
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} |
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``` |
