初始化项目,由ModelHub XC社区提供模型
Model: AI-ModelScope/MolGen-7b Source: Original Platform
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92
README.md
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README.md
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---
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license: apache-2.0
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pipeline_tag: text-generation
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tags:
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- chemistry
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- biology
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- text-generation-inference
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---
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## 💡 Model description
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This repo contains a large molecular generative model built with molecular language SELFIES.
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## 🔍 Intended uses
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You can use the model to generate molecules from scratch (i.e., inputting the bos_token), or input a partial structure for the model to complete.
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## 🛠️ How to use
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We have provided two types of examples. You can modify the input, generation parameters, etc., according to your needs.
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- Denovo molecule generation example:
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```python
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from modelscope import AutoTokenizer, AutoModelForCausalLM
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import torch
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tokenizer = AutoTokenizer.from_pretrained("AI-ModelScope/MolGen-7b")
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model = AutoModelForCausalLM.from_pretrained(
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"AI-ModelScope/MolGen-7b",
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load_in_8bit=True,
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torch_dtype=torch.float16,
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device_map="auto",
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)
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device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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sf_input = tokenizer(tokenizer.bos_token, return_tensors="pt").to(device)
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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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do_sample=True,
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max_new_tokens=10,
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top_p=0.75,
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top_k=30,
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return_dict_in_generate=False,
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num_return_sequences=5,
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)
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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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['[C][C][=C][C][=C][Branch2][Ring1][=Branch2][C][=Branch1]',
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'[C][N][C][C][C][Branch2][Ring2][Ring2][N][C]',
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'[C][O][C][=C][C][=C][C][Branch2][Ring1][Branch1]',
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'[C][N][C][C][C@H1][Branch2][Ring1][Branch2][N][Branch1]',
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'[C][=C][C][Branch2][Ring1][#C][C][=Branch1][C][=O]']
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```
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- Molecular completion example:
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```python
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from modelscope import AutoTokenizer, AutoModelForCausalLM
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import torch
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tokenizer = AutoTokenizer.from_pretrained("AI-ModelScope/MolGen-7b")
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model = AutoModelForCausalLM.from_pretrained(
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"AI-ModelScope/MolGen-7b",
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load_in_8bit=True,
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torch_dtype=torch.float16,
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device_map="auto",
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)
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device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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sf_input = tokenizer("[C][N][O]", return_tensors="pt").to(device)
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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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do_sample=True,
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max_new_tokens=10,
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top_p=0.75,
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top_k=30,
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return_dict_in_generate=False,
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num_return_sequences=5,
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)
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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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['[C][N][O][C][=Branch1][C][=O][/C][Ring1][=Branch1][=C][/C][=C]',
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'[C][N][O][/C][=Branch1][#Branch1][=C][/N][Branch1][C][C][C][C]',
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'[C][N][O][/C][=C][/C][=C][C][=Branch1][C][=O][C][=C]',
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'[C][N][O][C][=Branch1][C][=O][N][Branch1][C][C][C][=Branch1]',
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'[C][N][O][Ring1][Branch1][C][C][C][C][C][C][C][C]']
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```
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## 📚 Citation
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If you use our repository, please cite:
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```bibtex
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@article{fang2023molecular,
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title={Molecular Language Model as Multi-task Generator},
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author={Fang, Yin and Zhang, Ningyu and Chen, Zhuo and Fan, Xiaohui and Chen, Huajun},
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journal={arXiv preprint arXiv:2301.11259},
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year={2023}
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}
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```
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added_tokens.json
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{
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"<mask>": 184,
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"[#Branch1]": 12,
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"[#Branch2]": 178,
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"[#C-1]": 181,
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"[#C]": 165,
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"[#N+1]": 120,
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"[#N]": 23,
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"[#P]": 87,
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"[#Ring1]": 128,
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"[#S]": 40,
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"[-/Ring1]": 129,
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"[-/Ring2]": 156,
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"[-\\Ring1]": 164,
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"[-\\Ring2]": 34,
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"[/123I]": 7,
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"[/B]": 125,
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"[/Br]": 149,
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"[/C-1]": 68,
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"[/C@@H1]": 13,
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"[/C@@]": 14,
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"[/C@H1]": 177,
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"[/C@]": 31,
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"[/CH0]": 126,
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"[/CH1-1]": 88,
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"[/CH1]": 10,
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"[/C]": 118,
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"[/Cl]": 155,
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"[/F]": 6,
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"[/I]": 83,
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"[/N+1]": 152,
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"[/NH0]": 55,
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"[/NH1]": 24,
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"[/N]": 67,
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"[/O-1]": 171,
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"[/OH0]": 174,
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"[/O]": 69,
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"[/P@@]": 16,
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"[/P]": 79,
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"[/S+1]": 47,
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"[/S@@+1]": 21,
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"[/S@@]": 160,
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"[/S@]": 77,
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"[/S]": 112,
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"[/Si]": 38,
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"[11CH3]": 107,
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"[123I]": 124,
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"[124I]": 136,
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"[125I]": 39,
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"[127I]": 36,
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"[17F]": 143,
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"[18F]": 97,
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"[18OH1]": 76,
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"[3H]": 137,
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"[=B]": 25,
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"[=Branch1]": 33,
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"[=Branch2]": 100,
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"[=CH0]": 78,
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"[=C]": 35,
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"[=N+1]": 144,
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"[=N-1]": 161,
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"[=NH0]": 27,
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"[=N]": 105,
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"[=O+1]": 96,
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"[=O]": 30,
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"[=P+1]": 98,
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"[=P@@H1]": 32,
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"[=P@@]": 53,
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"[=P@H1]": 147,
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"[=P@]": 157,
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"[=PH1]": 132,
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"[=P]": 86,
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"[=Ring1]": 163,
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"[=Ring2]": 52,
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"[=S+1]": 133,
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"[=S@+1]": 167,
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"[=S@@+1]": 42,
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"[=S@@H1]": 106,
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"[=S@@]": 5,
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"[=S@]": 44,
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"[=SH1]": 117,
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"[=S]": 73,
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"[B-1]": 122,
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"[B@-1]": 179,
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"[B@@-1]": 17,
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"[B@@H1-1]": 56,
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"[B@H1-1]": 121,
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"[BH1-1]": 54,
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"[BH2-1]": 91,
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"[BH3-1]": 75,
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"[B]": 108,
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"[Br+1]": 166,
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"[Br]": 62,
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"[Branch1]": 104,
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"[Branch2]": 140,
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"[C+1]": 65,
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"[C-1]": 8,
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"[C@@H1]": 15,
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"[C@@]": 173,
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"[C@H1]": 29,
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"[C@]": 9,
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"[CH0]": 28,
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"[CH1+1]": 41,
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"[CH1-1]": 4,
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"[CH1]": 115,
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"[CH2-1]": 110,
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"[CH2]": 146,
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"[C]": 139,
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"[Cl]": 11,
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"[F+1]": 50,
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"[F]": 66,
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"[I]": 63,
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"[N+1]": 150,
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"[N-1]": 84,
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"[N@+1]": 111,
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"[N@@+1]": 131,
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"[N@@H1+1]": 162,
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"[NH0]": 148,
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"[NH1]": 130,
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"[N]": 19,
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"[O+1]": 85,
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"[O-1]": 58,
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"[OH0]": 71,
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"[O]": 20,
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"[P+1]": 82,
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"[P@+1]": 158,
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"[P@@+1]": 94,
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"[P@@H1]": 170,
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"[P@@]": 59,
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"[P@H1]": 81,
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"[P@]": 175,
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"[PH1]": 134,
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"[PH2]": 51,
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"[P]": 80,
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"[Ring1]": 70,
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"[Ring2]": 90,
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"[S+1]": 61,
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"[S@+1]": 72,
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"[S@@+1]": 57,
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"[S@@H1]": 45,
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"[S@@]": 154,
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"[S@]": 93,
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"[SH0]": 182,
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"[SH1]": 123,
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"[SH2]": 101,
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"[SH3]": 102,
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"[S]": 60,
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"[Si]": 119,
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"[Sn+2]": 183,
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"[Sn+3]": 135,
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"[SnH1]": 109,
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"[SnH2]": 99,
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"[Sn]": 114,
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"[\\123I]": 89,
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"[\\B-1]": 64,
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"[\\B]": 159,
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"[\\Br]": 142,
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"[\\C-1]": 127,
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"[\\C@@H1]": 22,
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"[\\C@@]": 46,
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"[\\C@H1]": 49,
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"[\\C@]": 145,
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"[\\CH0]": 176,
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"[\\CH1-1]": 153,
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"[\\C]": 43,
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"[\\Cl]": 37,
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"[\\F]": 26,
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"[\\I]": 172,
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"[\\N+1]": 92,
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"[\\NH1]": 103,
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"[\\N]": 138,
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"[\\O-1]": 141,
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"[\\O]": 18,
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"[\\P@@]": 113,
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"[\\P]": 74,
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"[\\S+1]": 95,
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"[\\S@@+1]": 169,
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"[\\S@@]": 180,
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"[\\S@]": 116,
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"[\\SH1]": 151,
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"[\\S]": 48,
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"[\\Si]": 168
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}
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config.json
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{
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"_name_or_path": "/newdisk3/data/fangyin/molgen-7b",
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"architectures": [
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"LlamaForCausalLM"
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],
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"bos_token_id": 0,
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"eos_token_id": 2,
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"hidden_act": "silu",
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"hidden_size": 4096,
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"initializer_range": 0.02,
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"intermediate_size": 11008,
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"max_position_embeddings": 2048,
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"max_sequence_length": 2048,
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"model_type": "llama",
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"num_attention_heads": 32,
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"num_hidden_layers": 32,
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"num_key_value_heads": 32,
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"pad_token_id": 1,
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"rms_norm_eps": 1e-06,
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"tie_word_embeddings": false,
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"torch_dtype": "float32",
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"transformers_version": "4.28.1",
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"use_cache": false,
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"vocab_size": 185
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}
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configuration.json
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configuration.json
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{"framework": "pytorch", "task": "text-generation", "allow_remote": true}
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generation_config.json
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{
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"_from_model_config": true,
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"bos_token_id": 0,
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"eos_token_id": 2,
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"pad_token_id": 1,
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||||||
|
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||||||
33
special_tokens_map.json
Normal file
33
special_tokens_map.json
Normal file
@@ -0,0 +1,33 @@
|
|||||||
|
{
|
||||||
|
"bos_token": "<s>",
|
||||||
|
"cls_token": {
|
||||||
|
"content": "<s>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"eos_token": "</s>",
|
||||||
|
"mask_token": {
|
||||||
|
"content": "<mask>",
|
||||||
|
"lstrip": true,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"pad_token": "<pad>",
|
||||||
|
"sep_token": {
|
||||||
|
"content": "</s>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"unk_token": {
|
||||||
|
"content": "<unk>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
}
|
||||||
|
}
|
||||||
1714
tokenizer.json
Normal file
1714
tokenizer.json
Normal file
File diff suppressed because it is too large
Load Diff
64
tokenizer_config.json
Normal file
64
tokenizer_config.json
Normal file
@@ -0,0 +1,64 @@
|
|||||||
|
{
|
||||||
|
"add_prefix_space": false,
|
||||||
|
"bos_token": {
|
||||||
|
"__type": "AddedToken",
|
||||||
|
"content": "<s>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"clean_up_tokenization_spaces": true,
|
||||||
|
"cls_token": {
|
||||||
|
"__type": "AddedToken",
|
||||||
|
"content": "<s>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"eos_token": {
|
||||||
|
"__type": "AddedToken",
|
||||||
|
"content": "</s>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"errors": "replace",
|
||||||
|
"mask_token": {
|
||||||
|
"__type": "AddedToken",
|
||||||
|
"content": "<mask>",
|
||||||
|
"lstrip": true,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"model_max_length": 1024,
|
||||||
|
"pad_token": {
|
||||||
|
"__type": "AddedToken",
|
||||||
|
"content": "<pad>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"sep_token": {
|
||||||
|
"__type": "AddedToken",
|
||||||
|
"content": "</s>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
},
|
||||||
|
"tokenizer_class": "BartTokenizer",
|
||||||
|
"trim_offsets": true,
|
||||||
|
"unk_token": {
|
||||||
|
"__type": "AddedToken",
|
||||||
|
"content": "<unk>",
|
||||||
|
"lstrip": false,
|
||||||
|
"normalized": true,
|
||||||
|
"rstrip": false,
|
||||||
|
"single_word": false
|
||||||
|
}
|
||||||
|
}
|
||||||
1
vocab.json
Normal file
1
vocab.json
Normal file
@@ -0,0 +1 @@
|
|||||||
|
{"<s>":0,"<pad>":1,"</s>":2,"<unk>":3}
|
||||||
Reference in New Issue
Block a user