ProteinNPT

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Error when running zero_shot_fitness_tranception.py: No such file or directory

1

Hi @pascalnotin I encountered an error while running the `zero_shot_fitness_tranception.py` through `zero_shot_fitness_subs.sh`: ``` Traceback (most recent call last): File "home/ProteinNPT-master/scripts/zero_shot_fitness_tranception.py", line 116, in main() File "home/ProteinNPT-master/scripts/zero_shot_fitness_tranception.py", line 46, in main...

BoyangLi-NKU

num_MSA_sequences

1

Does num_MSA_sequences affect the final result? I retrained proteinnpt on assay IF1_ECOLI_Kelsic_2016 with msat, but got spearman 0.614.

ZhummCrow

Error loading main sequence embeddings

12

Hi everyone, Im trying to train a new model with my own data. Step 1 (computing embeddings) and 2 (zero-shot) are running perfectly, but step 3 is complaining about missing...

dc2211

Hi there, Could you provide more details about the training set? In the ProteinNPT paper, you mention optimizing the model's hyperparameters using validation dataset. However, in the ProteinGym benchmark dataset,...

Meron-TANG

fine-tuning with more protein sequences

1

Hi, I have a corpus of about 500,000 protein sequences and would like to apply them to existing models like ESM2 or this one for predicting the fitness effect of...

avilella

Hi there! Thanks for this great work. I'm wondering if you have the code for fitness conditional sampling new sequence variants that you addressed in the paper with GFP variants....

TheMatrixMaster