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README.md

@@ -69,7 +69,7 @@ Pretrained on deduplicated peptide sequences from:
 
 | R² | Pearson | RMSE | MAE |
 |:--:|:-------:|:----:|:---:|
-| 0.758 | 0.871 | 0.384 | 0.283 |
+| 0.759 | 0.872 | 0.383 | 0.277 |
 
 Train/test 9:1, val 10% from train.
 
@@ -77,8 +77,8 @@ Train/test 9:1, val 10% from train.
 
 | Split | ROC-AUC | PR-AUC | F1 | MCC | Balanced Acc |
 |:-----:|:-------:|:------:|:--:|:---:|:------------:|
-| Random | 0.964 | 0.886 | 0.826 | 0.784 | 0.887 |
-| aCSM | 0.870 | 0.700 | 0.608 | 0.549 | 0.734 |
+| Random | 0.970 | 0.913 | 0.860 | 0.824 | 0.912 |
+| aCSM | 0.876 | 0.717 | 0.597 | 0.552 | 0.723 |
 
 Train/test 8:2, val 10% from train, 1:4 positive:negative ratio.
 - **Random**: random split

config.json

@@ -31,6 +31,6 @@
   "position_buckets": 256,
   "sep_token_id": 2,
   "share_att_key": false,
-  "transformers_version": "4.57.3",
+  "transformers_version": "5.3.0",
   "vocab_size": 78
 }

model.safetensors

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:c5845d9c0b3b1e5948487e870ccbc1790ec9e2d28c07a7dcf124a913a5ec8153
-size 219166144
+oid sha256:af4f60f03ddf756a4e03cb0b776762cdbcd6d4d770c5ade44aa29db767d35371
+size 219405856

modeling_helmbert.py

@@ -861,7 +861,7 @@ class HELMBertForMaskedLM(HELMBertPreTrainedModel):
         >>> predictions = outputs.logits.argmax(dim=-1)
     """
 
-    _tied_weights_keys = ["lm_head.decoder.weight"]
+    _tied_weights_keys = {"lm_head.decoder.weight": "helmbert.embeddings.word_embeddings.weight"}
 
     def __init__(self, config: HELMBertConfig):
         super().__init__(config)