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enai4bio / DeepAAI

DeepAAI
GNU Affero General Public License v3.0
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hi，I have a problem about training with baseline methods. It notices that "AttributeError: 'AbsDataset' object has no attribute 'raw_all_antibody_set_len'. " #2

Open wyf111 opened 1 year ago

wyf111 commented 1 year ago

hi，I have a problem about training with baseline methods. It says that "AttributeError: 'AbsDataset' object has no attribute 'raw_all_antibody_set_len'. " Hope you can add this module. Thank you.

stzhangjie commented 1 year ago

As a processed feature file, "abs_dataset_cls_antibody=344_virus=912_kmer_min_df=0.1__protein_ft_dict.pkl " is provided in the format of tar.gz and needs to be decompressed for re-training.

wyf111 commented 1 year ago

Thank you very much for your reply. I have depressed the file, but still couldn't find the function.

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tb1over commented 1 year ago

raw_all_antibody_set_len

this attribute is not in this pkl file,

tb1over commented 1 year ago

{'antibody_one_hot': tensor([[[0.0000, 0....0.0455]]]), 'virus_one_hot': tensor([[[1.0000, 0....0.0455]]]), 'antibody_pssm': tensor([[3.7251, 3.9... 4.6578]]), 'virus_pssm': tensor([[1.8888, 2.5... 1.9118]]), 'antibody_amino_num': tensor([[ 3, 7, 8,... 21, 21]]), 'virus_amino_num': tensor([[ 0, 11, 6,... 21, 21]]), 'antibody_kmer_whole': tensor([[-1.8321, -1...-0.8420]]), 'virus_kmer_whole': tensor([[ 0.7285, 0...-0.8420]])}

it just have the data in abs_dataset_cls_antibody=344_virus=912_kmer_min_df=0.1__protein_ft_dict.pkl file above, i do not know where to find raw_all_antibody_set_len and raw_all_virus_set_len.

Thank you !