commit 6dd5bb7b8d117c82d06993bac2dbbdce921c7bad Author: ModelHub XC Date: Sat May 30 23:22:19 2026 +0800 初始化项目，由ModelHub XC社区提供模型 Model: wudejian789/MolMetaLM-base Source: Original Platform diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..a6344aa --- /dev/null +++ b/.gitattributes @@ -0,0 +1,35 @@ +*.7z filter=lfs diff=lfs merge=lfs -text +*.arrow filter=lfs diff=lfs merge=lfs -text +*.bin filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.ckpt filter=lfs diff=lfs merge=lfs -text +*.ftz filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.h5 filter=lfs diff=lfs merge=lfs -text +*.joblib filter=lfs diff=lfs merge=lfs -text +*.lfs.* filter=lfs diff=lfs merge=lfs -text +*.mlmodel filter=lfs diff=lfs merge=lfs -text +*.model filter=lfs diff=lfs merge=lfs -text +*.msgpack filter=lfs diff=lfs merge=lfs -text +*.npy filter=lfs diff=lfs merge=lfs -text +*.npz filter=lfs diff=lfs merge=lfs -text +*.onnx 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-0,0 +1,26 @@ +--- +pipeline_tag: text-generation +tags: +- Molecule Language Model +- Physicochemical Knowledge +--- + +refer to https://github.com/CSUBioGroup/MolMetaLM for more details. + +# Usage + +## Prepare tokenizer and model +```python +from transformers import AutoTokenizer, AutoModel +tokenizer = AutoTokenizer.from_pretrained('wudejian789/MolMetaLM-base') +model = AutoModel.from_pretrained('wudejian789/MolMetaLM-base') +``` + +## Obtain molecular representations from SMILES +```python +smi = "COc1cc2c(cc1OC)CC([NH3+])C2" +tokenized_smi = tokenizer(" ".join(list(smi)), return_token_type_ids=False, + return_tensors='pt', max_length=512, padding='longest', truncation=True) +emb_smi = model(**tokenized_smi).last_hidden_state +print(emb_smi.shape) # batch size, seq length, embedding size +``` diff --git a/added_tokens.json b/added_tokens.json new file mode 100644 index 0000000..9662eac --- /dev/null +++ b/added_tokens.json @@ -0,0 +1,782 @@ +{ + ",": 489, + ";": 488, + 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"806": { + "content": "[(XYZ)ATOM:Pr]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "807": { + "content": "[(XYZ)ATOM:Pt]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "808": { + "content": "[(XYZ)ATOM:Pu]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "809": { + "content": "[(XYZ)ATOM:Rb]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "810": { + "content": "[(XYZ)ATOM:Re]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "811": { + "content": "[(XYZ)ATOM:Rh]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "812": { + "content": "[(XYZ)ATOM:Rn]", + "lstrip": false, + "normalized": true, + "rstrip": false, 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false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "820": { + "content": "[(XYZ)ATOM:Sn]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "821": { + "content": "[(XYZ)ATOM:Sr]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "822": { + "content": "[(XYZ)ATOM:Ta]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "823": { + "content": "[(XYZ)ATOM:Tb]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "824": { + "content": "[(XYZ)ATOM:Tc]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "825": { + "content": "[(XYZ)ATOM:Te]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + 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false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "840": { + "content": "[FPR:ECFP]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "841": { + "content": "[FPR:FCFP]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "842": { + "content": "[FPR:Avalon]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "843": { + "content": "[SEP]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": true + }, + "844": { + "content": "[SPAN]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "845": { + "content": "[VALUE]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "846": { + "content": "[XYZ]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "847": { + "content": "[BITS]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "848": { + "content": "[CUSPRO]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "849": { + "content": "[SUB]", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": false, + "special": false + }, + "850": { + "content": "[CLS]", + "lstrip": false, + "normalized": false, + "rstrip": false, + "single_word": false, + "special": true + } + }, + "clean_up_tokenization_spaces": true, + "cls_token": "[CLS]", + "do_lower_case": false, + "mask_token": "[MASK]", + "model_max_length": 1000000000000000019884624838656, + "pad_token": "[PAD]", + "sep_token": "[SEP]", + "strip_accents": null, + "tokenize_chinese_chars": true, + "tokenizer_class": "BertTokenizer", + "unk_token": "[UNK]" +} diff --git a/vocab.txt b/vocab.txt new file mode 100644 index 0000000..8958bd7 --- /dev/null +++ b/vocab.txt @@ -0,0 +1,71 @@ +[PAD] +[SOS] +[EOS] +[UNK] +[MASK] +# +( +) ++ +- +. +/ +0 +1 +2 +3 +4 +5 +6 +7 +8 +9 += +@ +A +B +C +D +E +F +G +H +I +K +L +M +N +O +P +R +S +T +U +V +W +X +Y +Z +[ +\ +] +a +b +c +d +e +f +g +h +i +k +l +m +n +o +p +r +s +t +u +y