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🛠️ Added support for PeptideMTR_lg model #158

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Merged
RaulFD-creator merged 2 commits into from
Jan 30, 2026
Merged

🛠️ Added support for PeptideMTR_lg model #158

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a2b926d
🛠️ Added support for PeptideMTR_lg model
RaulFD-creator Jan 30, 2026
97911d2
🚀 v.2.0.5
RaulFD-creator Jan 30, 2026
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13 changes: 10 additions & 3 deletions autopeptideml/reps/lms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,8 @@
'MoLFormer-XL-both-10pct': 768,
'ChemBERTa-77M-MLM': 384,
'ChemBERTa-100M-MLM': 768,
'PeptideCLM-23M-all': 768
'PeptideCLM-23M-all': 768,
'PeptideMTR_lg': 1024,
}

SYNONYMS = {
Expand All @@ -55,7 +56,8 @@
'molformer-xl': 'MoLFormer-XL-both-10pct',
'chemberta-2': 'ChemBERTa-77M-MLM',
'chemberta-3': 'ChemBERTa-100M-MLM',
'peptideclm': 'PeptideCLM-23M-all'
'peptideclm': 'PeptideCLM-23M-all',
'peptidemtr': "PeptideMTR_lg",
}


Expand Down Expand Up @@ -198,10 +200,12 @@ def _load_model(self, model: str):
elif 'ankh' in model.lower():
self.lab = 'ElnaggarLab'
elif 'molformer' in model.lower():
print("Warning: Molformer does not support transformers>=5.0.0, we recommend using an earlier version, e.g., transformers==4.41.2")
self.lab = 'ibm'
elif 'chemberta' in model.lower():
self.lab = 'DeepChem'
elif 'clm' in model.lower():
elif (('clm' in model.lower() or 'mtr' in model.lower()) and
'peptide' in model.lower()):
self.lab = 'aaronfeller'
if 't5' in model.lower():
self.tokenizer = T5Tokenizer.from_pretrained(f'Rostlab/{model}',
Expand Down Expand Up @@ -309,7 +313,10 @@ def _rep_batch(
attention_mask=inputs['attention_mask'],
decoder_input_ids=inputs['input_ids']
).last_hidden_state
elif 'peptidemtr' in self.model_name.lower():
embd_rpr = self.model(**inputs)['last_layer']
else:
print(self.model(**inputs))
embd_rpr = self.model(**inputs).last_hidden_state
output = []
for idx in range(len(batch)):
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -73,6 +73,6 @@ def get_files_in_dir(path: Path, base: Path) -> list:
name='autopeptideml',
packages=find_packages(exclude=['examples']),
url='https://ibm.github.io/AutoPeptideML/',
version='2.0.4',
version='2.0.5',
zip_safe=False,
)