zjunlp/OntoProtein

Issues

• Issues regarding the usage of the ProtBERT tokenizer on multi-fasta-files

  #34 opened 2 months ago by QuadratJunges
  3

• Question: Is it possible get the embedding of the relations and entities separately using Ontoprotein ?

  #33 opened 2 months ago by anonimoustt
  6

• Generating Embedding of Protein Sequence

  #30 opened 10 months ago by anonimoustt
  11

• Important relation for the protein sequence

  #32 opened 10 months ago by anonimoustt
  3

• Question: What is the evaluation metric for protein function classification?

  #31 opened a year ago by boram915
  2

• Running Code in Google Colab

  #29 opened a year ago by anonimoustt
  14

• Inconsistent data statistics between the downloaded dataset and the reported statistics

  #28 opened a year ago by acharkq
  2

• Go-Go relations are the same as Protein-Go relations?

  #27 opened 2 years ago by xinghao302001
  5

• Exploding KE loss when training a new `protein-go` set

  #26 opened 2 years ago by jasperhyp
  1

• Question about computing resource and batch size

  #24 opened 2 years ago by jasperhyp
  4

• Rationale for choosing this loss function

  #25 opened 2 years ago by jasperhyp
  2

• [Confirmation] Optimal Hyperparameters and Reproducibility

  #21 opened 2 years ago by chao1224
  19

• What is the `OntoModel` referenced in `run_pretrain.sh`

  #23 opened 2 years ago by tomcobley
  1

• ImportError in deepspeed.py

  #22 opened 2 years ago by tomcobley
  2

• 关于GO的embedding

  #16 opened 2 years ago by liutong19991016
  1

• Graph knowledge creation

  #19 opened 2 years ago by Amels404
  1

• Trainer problem for pre-training

  #20 opened 2 years ago by nihaowxh
  2

• Computational Resources and Time

  #9 opened 3 years ago by sa5r
  4

• 关于GO prediction的表现

  #18 opened 2 years ago by jasperhyp
  1

• 请问是否有和ESM-1b的benchmark结果

  #17 opened 2 years ago by jasperhyp
  1

• the problem of biopython version?

  #15 opened 2 years ago by nihaowxh
  1

• goa_uniprot_all.gaf和goa_uniprot_all.gat有什么不同?

  #13 opened 2 years ago by xinghao302001
  1

• ontoProtein pretrained model

  #14 opened 2 years ago by wenyuhaokikika
  4

• Issue in creating an environment for OntoProtein pretraining

  #12 opened 2 years ago by amalislam675
  5

• run_pretrain.sh 报错

  #11 opened 3 years ago by Seyfried97
  4

• 预训练数据缺失问题

  #10 opened 3 years ago by Seyfried97
  2

• run_contact.sh error

  #8 opened 3 years ago by sa5r
  7

• Cannot run the code without GPU

  #6 opened 3 years ago by sa5r
  1

• No such file or directory 'protein_go_train_triplet_filtered.txt'

  #7 opened 3 years ago by sa5r
  1

• goatools包问题

  #5 opened 3 years ago by lonetravelwolf
  7

• 数据文件

  #4 opened 3 years ago by lonetravelwolf
  2

• No module named 'transformers.deepspeed'

  #3 opened 3 years ago by yuzhiguo07
  2

• Backward Error during Pre-training

  #2 opened 3 years ago by chang-github-00
  1