Comments (1)
nadavbra
commented on July 24, 2024
Hi @awesome-crab,
In principle you should be able to train ProteinBERT without GO annotations. You can either feed it with all-zero vectors or any other global features that seem appropriate for your specific use-case. However, the current scripts assume that you create an h5 dataset from UniRef (with GO annotations).
If you are comfortable with writing a little bit of Python code, I think the best solution for you would be to skip the pretraining script and pretrain ProteinBERT using the Python API (using the functions in the pretraining submodule). Specifically I imagine you'd want to override DatasetHandler to load sequences from your file instead of an h5 dataset.
BTW, it's funny that you are interested in training a protein language model for TCR sequences. I've considered working on a very similar project myself. If you think you might be open for collaboration, feel free to send me an email :)
(Of course, if you want to continue working on this project on your own, that's perfectly understandable.)
Best,
Nadav Brandes
from protein_bert.
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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