Load pretrained weights and cleanup config for stage 1

stage1_config.json

@@ -28,14 +28,14 @@
     "base_lr": 0.0016,
     "global_batch_size": 80,
     "lr": 0.0005,
-    "seq_model_path": "/project/ranganathanr/niksapraljak/TextDiff_model_weights/Stage_1/pretrained_models/esm2_t33_650M_UR50D.pt",
+    "seq_model_path": "/project/ranganathanr/niksapraljak/HF_repo/HF_BioM3_project/BioM3/weights/LLMs/esm2_t33_650M_UR50D.pt",
     "pretrained_seq": true,
     "trainable_seq": true,
     "rep_layer": 33,
     "protein_encoder_embedding": 1280,
     "protein_encoder_lr": 0.0005,
     "pLM_n_layers_to_finetune": 1,
-    "text_model_path": "/project/ranganathanr/niksapraljak/TextDiff_model_weights/Stage_1/pretrained_models/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext",
+    "text_model_path": "/project/ranganathanr/niksapraljak/HF_repo/HF_BioM3_project/BioM3/weights/LLMs/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext",
     "pretrained_text": true,
     "trainable_text": true,
     "text_encoder_embedding": 768,
@@ -47,4 +47,4 @@
     "head_lr": 0.0005,
     "inference_data_path": "/project/ranganathanr/niksapraljak/BioM3_PDZ/data/test_prompts_PDZ_swissprot_pfam_dataset.csv",
     "inference_output_path": "/project/ranganathanr/niksapraljak/BioM3_PDZ/outputs/Stage1_test_prompts_PDZ.pt"
-}
+}

weights/LLMs/README.md

@@ -12,9 +12,16 @@ This folder contains the pre-trained weights for the **ESM2** and **PubMedBERT**
 To download the ESM2 (650M parameter) model weights:
 ```bash
 wget https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t33_650M_UR50D.pt
+wget https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t33_650M_UR50D-contact-regression.pt
 ```
 
 ### PubMedBERT Model
+
+Make sure large-file storage capabilities are installed in your environment before cloning HuggingFace model card.
+```bash
+git lfs install 
+```
+
 To download the PubMedBERT model weights:
 ```bash
 git clone https://huggingface.co/microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext