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License: Apache License 2.0
The official implementation of "Improving Antibody Humanness Prediction using Patent Data".
License: Apache License 2.0
Hello, thanks for the good tool. I had some issues with installing dependencies, but made it work with Docker. Here is a Dockerfile.txt (extension added so upload is allowed) if someone finds it useful to build a tool in a container environment like Docker.
However, when I ran selfpad_eval.py to evaluate humanness I am getting this error:
Building the models for training and evaluation in SubTab framework...
Traceback (most recent call last):
File "/opt/SelfPAD/selfpad_eval.py", line 250, in <module>
main()
File "/opt/SelfPAD/selfpad_eval.py", line 224, in main
f1, recall, prec, auc, acc, pr_auc = eval(data_loader, config=config)
File "/opt/SelfPAD/selfpad_eval.py", line 45, in eval
model = PADFintune(config)
File "/opt/SelfPAD/src/selfpad_humanness.py", line 47, in __init__
self.set_autoencoder()
File "/opt/SelfPAD/src/selfpad_humanness.py", line 53, in set_autoencoder
self.transformer = PADFT(
File "/opt/SelfPAD/utils_finetune/model_utils.py", line 49, in __init__
self.transformer = SelfPAD.load_from_checkpoint(
File "/usr/local/lib/python3.9/site-packages/pytorch_lightning/utilities/model_helpers.py", line 100, in wrapper
return self.method(cls, *args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/pytorch_lightning/core/module.py", line 1561, in load_from_checkpoint
loaded = _load_from_checkpoint(
File "/usr/local/lib/python3.9/site-packages/pytorch_lightning/core/saving.py", line 61, in _load_from_checkpoint
checkpoint = pl_load(checkpoint_path, map_location=map_location)
File "/usr/local/lib/python3.9/site-packages/lightning_fabric/utilities/cloud_io.py", line 55, in _load
with fs.open(path_or_url, "rb") as f:
File "/usr/local/lib/python3.9/site-packages/fsspec/spec.py", line 1293, in open
f = self._open(
File "/usr/local/lib/python3.9/site-packages/fsspec/implementations/local.py", line 184, in _open
return LocalFileOpener(path, mode, fs=self, **kwargs)
File "/usr/local/lib/python3.9/site-packages/fsspec/implementations/local.py", line 306, in __init__
self._open()
File "/usr/local/lib/python3.9/site-packages/fsspec/implementations/local.py", line 311, in _open
self.f = open(self.path, mode=self.mode)
FileNotFoundError: [Errno 2] No such file or directory: '/opt/SelfPAD/results/pretraining/training/model/pretrained_model.ckpt'
Input file I've used for testing is attached below. And this is the command line I've used:
python3 /opt/SelfPAD/selfpad_eval.py --evaluate therapeutic_ABs.selfpad_input
Can you help me figure out what the issue is?
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