Problem for training DeepBGC from scratch
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Description
Hi, Prihoda:
Here, I have some problems want to consult you. I try to train DeepBGC from scratch. According to the "Readme.md" file, I download the MIBiG.pfam.tsv and GeneSwap_Negatives.pfam.tsv files as the positive and negative samples. Then, I use to the following instruction to train DeepBGC:
deepbgc train --model deepbgc.json --output MyDeepBGCDetector.pkl MIBiG.pfam.tsv GeneSwap_Negatives.pfam.tsv
But, I met the error:
Why do we need to load "pfam2vec.csv" during training? I think this should be obtained from the trained model.
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Research direction
Start with Readme.md and the documented deepbgc train command, using MIBiG.pfam.tsv and GeneSwap_Negatives.pfam.tsv to reproduce the reported error. Trace why training loads pfam2vec.csv and determine whether the documentation or training workflow is incorrect; done means the cause and required correction are clearly documented.
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Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100