Comments (3)
nadavbra
commented on July 24, 2024
Hi @WilliamSawran ,
I want to start by making sure that you got the file ~/proteinbert_models/epoch_92400_sample_23500000.pkl in order.
What is the size of this file?
You can run ls -lh /proteinbert_models/epoch_92400_sample_23500000.pkl
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WilliamSawran
commented on July 24, 2024
Hi Nadavrbra,
FileZilla reported that the pkl file was transferred from your server to my local machine successfully. I trusted FileZilla and naively proceeded to run the protein_bert code. However, the size between my transferred pkl file (30MB) and your pkl file (187MB) was not the same. A colleague of mine was able to transfer for me your entire pkl file and I was able to load the pre-trained proteinbert model.
Sorry for any inconvenience and thank you for answering my message. I appreciate the prompt reply, especially since past researchers I've contacted via email don't respond at all. I was able to obtain the pkl file and load the pre-trained proteinbert model, so you can close this case.
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nadavbra
commented on July 24, 2024
I'm glad I could help. Good luck using the model!
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Related Issues (20)
- Failing to get the weights from the dedicated github repo HOT 5
- Use ProteinBERT with Own Dataset HOT 3
- Original h5 file HOT 5
- loss plot during pretraining HOT 1
- signal peptide detection HOT 1
- KeyError: "Unable to open object (object 'test_set_mask' doesn't exist)" HOT 6
- How to extract the embedding of an amino acid? HOT 10
- Graph execution error HOT 6
- Extract local and global representation using finetune model HOT 1
- Running Benchmarks HOT 4
- Evaluation on larger data set HOT 6
- Using vector representations in the "weights" parameter in the "embedding" section of an LSTM model after fine-tuning my own data HOT 1
- Failing to extract global embedding (1,15599) -> (1,512) HOT 1
- What do the settings mean? HOT 3
- Error when trying to run the finetuning code given in the jupyter notebook HOT 2
- ValueError, set_weights error
- model_generation.py list is not callable error HOT 2
- GO annotations during fine tuning HOT 1
- Missing MajorPTMs train CSV file HOT 1
- Can't get proteinBERT to run on GPU HOT 1
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