Comments (1)
Since our model is trained over additional amino acid codes (JOUBZX), it's possible to observe them at inference in your generations.
These are;
U = selenocysteine
O = pyrrolysine
B = D or N
J = I or L
Z = E or Q
X = unknown
It could be due to many reasons, it's not clear that the MSA would be the problem.
To prevent the model from predicting these amino acids at inference you can change line 257 and 259
evodiff/evodiff/generate_msa.py
Line 257 in 683b08d
to:
p = preds[:, random_x, random_y, :20]
this will force the model to only generate seqeunces using the first 20 amino acids in MSA_ALPHABET: ACDEFGHIKLMNPQRSTVWY
from evodiff.
Related Issues (20)
- Question about fine-tuning
- Using generate_msa() HOT 3
- Error Loading Pretrained Model with `--pretrained` Flag
- Allow diffusion to gap character in OADM models? HOT 1
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- Error Loading State Dictionary in ByteNetLMTime: Unexpected Keys HOT 6
- Error with IDR inpainting with Evodiff-MSA HOT 1
- Question on MaxHamming distance HOT 1
- the error in generate sequences using esm1b_650M HOT 2
- Running the `evodiff/generate.py` script HOT 1
- msa_oa_ar_maxsub not recognized HOT 2
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