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DeepChainBio
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bio-transformers
bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.
https://bio-transformers.readthedocs.io/en/latest/getting_started/install.html
Apache License 2.0
143
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ValueError: Connection error, and we cannot find the requested files in the cached path. Please try again or make sure your Internet connection is on.
#41
wbw1111
opened
1 month ago
1
chore: remove OS generated files
#40
johnhunter
closed
1 year ago
0
ERRO: ValueError: Connection error, and we cannot find the requested files in the cached path.
#39
githubXin123
closed
1 year ago
0
Feature Request - Use any ESM model
#38
DNA2RNA
opened
1 year ago
0
Replaced compute_ with compute_loglikelihood
#37
hunarbatra
opened
2 years ago
0
Develop
#36
delfosseaurelien
closed
2 years ago
0
bump transformers dependencies + fixed setup in windows environments
#35
hiddentn
closed
2 years ago
0
Saving and Loading Fine Tuned Model
#34
maggieelkin
opened
2 years ago
0
pytorch_lightning.utilities.exceptions.MisconfigurationException: You have asked for `amp_level='O2'` but it's only supported with `amp_backend='apex'`.
#33
OlfwayAdbayIgbay
opened
2 years ago
1
CONTRIBUTING - feedbacks / problems
#32
martinp7
opened
3 years ago
0
Fix typos docstring of get_batch_indices
#31
martinp7
closed
3 years ago
0
Wrong formatting in CONTRIBUTING.md - Git conventions
#30
martinp7
closed
3 years ago
1
Typo in docstring of get_batch_indices defined in biotransformers/lightning_utils/data.py
#29
martinp7
closed
3 years ago
0
improved indices sampling to get batches with fixed number of tokens
#28
delfosseaurelien
closed
3 years ago
0
Develop
#27
delfosseaurelien
closed
3 years ago
0
a worker died or was killed while executing a task by an unexpected system error
#26
wushixian
opened
3 years ago
6
How to use MSA transformer embeddings?
#25
wushixian
closed
3 years ago
2
ESM1v support
#24
idmjky
closed
3 years ago
2
fix: fix padding predictions in compute_accuracy
#23
ahmed-dj
closed
3 years ago
0
Still cannot use esm_msa1_t12_100M_UR50S, teturns the model not in the list.
#22
wushixian
closed
3 years ago
2
Can not import properly after newest version installation
#21
idmjky
closed
3 years ago
2
CUDA RUNTIME ERROR
#20
idmjky
closed
3 years ago
2
Check batch size in multigpu
#19
delfosseaurelien
closed
3 years ago
0
Develop
#18
delfosseaurelien
closed
3 years ago
0
Code Refactoring
#17
ranzenTom
closed
3 years ago
0
Trouble using Multi-GPU on cluster
#16
idmjky
closed
3 years ago
5
ædd compute probas
#15
ranzenTom
closed
3 years ago
0
Get probabilities dicts
#14
ranzenTom
closed
3 years ago
1
Potential overlap
#13
sacdallago
closed
3 years ago
1
embedding in ESM is not extracted from the last layer
#12
mathpluscode
closed
3 years ago
1
Add "full" pool_mode
#11
KevinEloff
closed
3 years ago
1
Replace pooling_list with pool_mode in docs
#10
theomeb
closed
3 years ago
0
Jb wip add compute logits
#9
jbsevestre
closed
3 years ago
0
Use absolute import instead of relative import
#8
mathpluscode
closed
3 years ago
1
Monitor code quality
#7
mathpluscode
closed
3 years ago
1
Use GitHub actions for test and release
#6
mathpluscode
closed
3 years ago
1
add options to save the embedding
#5
delfosseaurelien
opened
3 years ago
0
add jupyter example
#4
delfosseaurelien
opened
3 years ago
1
add finetuning method
#3
delfosseaurelien
closed
3 years ago
3
add multi-gpu support
#2
delfosseaurelien
closed
3 years ago
1
add multi-gpu support
#1
delfosseaurelien
closed
3 years ago
0